Document:

Second Loan Modification Agreement

 Exhibit 10.10B 
 SECOND LOAN MODIFICATION AGREEMENT 
 THIS SECOND LOAN MODIFICATION
AGREEMENT (this “Agreement”) is made and entered into as of February 14, 2012 by and among UNION BANK, N.A. (“Bank”), WAGEWORKS, INC., a Delaware corporation (“Borrower”) and MHM RESOURCES,
LLC, a Delaware limited liability company (“Closing Date Guarantor”), with respect to the following facts: 

RECITALS 

This Agreement is made and entered into in reliance on the following recitals, which are acknowledged by each Obligor and Bank to be true
and accurate: 
 A. Bank and Borrower have entered into that certain Commercial Credit Agreement dated as of
August 31, 2010 (as amended, modified, supplemented or restated from time to time, including by that certain First Loan Modification Agreement dated as of November 16, 2011, collectively, the “Loan Agreement”) pursuant to
which Bank agreed to provide to Borrower, on and subject to the terms and conditions set forth therein, a revolving credit facility for loans up to Fifty Million Dollars ($50,000,000). Borrower may have liabilities to Bank under other credit
facilities or bank or cash management products; Bank and Borrower intend that such other facilities shall not be affected by this Agreement and shall remain in full force and effect in all respects. Capitalized terms not defined herein shall have
the meanings assigned to them in the Loan Agreement. 
 B. To induce Bank to extend credit to Borrower, Closing Date
Guarantor has unconditionally guaranteed the payment and performance of all of the Borrower’s obligations to Bank pursuant to that certain Continuing Guaranty dated as of August 31, 2010 (as amended, modified, supplemented or restated from
time to time, collectively, the “MHM Guaranty”). 
 C. To secure, among other things, payment and
performance of all of Borrower’s indebtedness, liabilities and obligations to Bank and all of Closing Date Guarantor’s indebtedness, liabilities and obligations under the MHM Guaranty, each of Borrower and Closing Date Guarantor executed
and delivered to Bank that certain Security Agreement dated as of August 31, 2010 by and among Bank, Borrower and Closing Date Guarantor and an Intellectual Property Security Agreement, each dated as of August 31, 2010, pursuant to which
Borrower and Closing Date Guarantor each granted to Bank a security interest in substantially all of their respective properties and assets, other than Client Trust Accounts. 
 D. There are no written or oral agreements concerning or affecting the Revolving Loans between Obligors, on the one hand, and Bank, on the other, other than the Loan Documents. 

E. At Borrower’s request, Bank is willing to modify the Loan Documents as set forth herein, provided that the conditions set
forth herein are satisfied within the time periods required under this Agreement. 
 AGREEMENT 

NOW THEREFORE, in consideration of the foregoing and for other valuable consideration, the receipt and sufficiency of which are
hereby acknowledged, the parties hereto hereby agree as follows: 
 1. Incorporation of Recitals.
Each of the above recitals is incorporated herein as true and correct and is relied upon by each party to this Agreement in agreeing to the terms of this Agreement. 

  
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 2. Confirmation of Debt and Loan Documents. Borrower and each
other Obligor hereby ratifies, reaffirms and confirms all of the terms and conditions of the Loan Documents in all respects and hereby acknowledges that the Loan Documents are valid and enforceable obligations against Borrower and each other
Obligor, due and payable in full, without defenses, setoffs or counterclaims of any kind. The indebtedness evidenced by the Loan Documents is hereby acknowledged and admitted. Except as expressly set forth herein, this Agreement shall not alter,
modify, amend, or in any way affect any of the terms, conditions, obligations, covenants, or agreements contained in the Loan Agreement or any other Loan Document. This Agreement shall not operate as a waiver of any right, power, or remedy of Bank
under the Loan Agreement or any other Loan Document. Borrower and each other Obligor hereby confirm that all obligations of Borrower and each other Obligor to Bank are secured by a perfected, first-priority security interest in the Collateral.

 3. Conditions Precedent. Each Obligor understands that this Agreement shall not be effective
and Bank shall have no obligation to amend the terms of the Loan Documents as provided herein, unless and until each of the following conditions precedent has been satisfied not later than December 30, 2011, or waived by Bank (in Bank’s
sole discretion): 
 (a) Each Obligor shall have executed and delivered to Bank this
Agreement. 
 (b) The representations and warranties of each Obligor under the Loan
Agreement, this Agreement and each other Loan Documents, as applicable, shall be true and correct as of the date hereof (except to the extent such representations and warranties expressly refer to an earlier date, in which case they are true,
correct and complete as of such earlier date). 
 (c) Borrower shall have reimbursed Bank
for Bank’s costs and expenses, including, without limitation, reasonable attorneys’ fees and expenses (including the fees of Bank’s in-house legal counsel and staff), incurred in connection with the negotiation and drafting of this
Agreement and the transactions contemplated hereby. 
 (d) On or before such time as Bank
may require, Borrower and each other Obligor shall have taken any and all actions and executed and delivered to Bank any and all documents necessary or appropriate in Bank’s sole discretion to effectuate this Agreement. 

4. Limited Waiver. Bank hereby waives any Event of Default occurring under the Loan Documents existing as
of the date hereof due to the fact that Borrower did not comply with the requirements of clause (i) of Section 9.16(m) and Section 9.29 of the Loan Agreement prior to January 15, 2012 with respect to Planned Benefit Systems
Incorporated, a Colorado corporation. This waiver applies only to the specific instance described above, and is not a waiver of any subsequent breach of the same provisions of the Loan Agreement, nor is it a waiver of any breach of any other
provision of the Loan Agreement. Further, Bank reserves all of the rights, powers and remedies available under the Loan Agreement and any other contracts or instruments executed by Borrower, including the right to cease making advances to Borrower
and to accelerate any or all of Borrower’s indebtedness if any subsequent breach of the same provision or any other provision of the Credit Agreement should occur. Bank is not obligated to

  
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grant this or any other waiver, consent or modification. No course of dealing on the part of Bank or any of its officers, nor any failure or delay in the exercise of any right by Bank, shall
operate as a waiver thereof, and any single or partial exercise of any such right shall not preclude any later exercise of any such right. Bank’s failure at any time to require strict performance by Borrower of any provision of any Loan
Document shall not affect any right of Bank thereafter to demand strict compliance and performance. Any suspension or waiver of a right must be in writing signed by an officer of Bank in accordance with the terms of the Loan Agreement. 

5. Modification of Loan Documents. To induce Bank to enter into this Agreement, Borrower agrees that the Loan
Documents are hereby supplemented and modified as follows, which modifications shall supersede and prevail over any conflicting provisions of the Loan Documents: 

(a) The definition of “Material Subsidiary” in Section 1.7 of the Loan Agreement is
hereby amended by adding the following at the end of such definition: 
 “Notwithstanding the foregoing,
PBS shall not be deemed to be a Material Subsidiary for purposes of Section 4 or Section 9.29 hereof until such time as PBS becomes a 5% Subsidiary.” 

(b) Section 9.16 of the Loan Agreement is hereby amended by amending and restating clause
(m) thereof to read as follows: 
 “(m) until such time as PBS becomes a 5% Subsidiary,
the security interest granted by PBS to Revere Corporate Center, L.L.C., a Colorado limited liability company (“Revere”) pursuant to Section 30 of that certain Office Lease, dated as of May 3, 2006 by and between PBS and
Revere, in the form provided to Bank on November 10, 2011; provided however, upon PBS becoming a 5% Subsidiary, such security interest shall be terminated and released to the satisfaction of Bank, and shall no longer qualify as a
Permitted Lien hereunder.” 
 (c) The Loan Agreement is hereby amended by amending
and restating Section 9.29 to read as follows: 
 “9.29 Subsidiaries. Borrower shall, and
shall cause each Material Subsidiary to, timely comply with the requirements of Section 4 hereof. Notwithstanding the foregoing, upon PBS becoming a 5% Subsidiary, Borrower and PBS shall take all such actions and shall execute and deliver to
Bank all such documents, instruments, agreements and certificates as Bank may require to make PBS an Obligor and to provide Bank with a perfected, first-priority security interest in substantially all assets and properties of PBS, including,
execution and delivery to Bank of a Continuing Guaranty, Security Agreement and Intellectual Property Security Agreement, in each case in form and substance satisfactory to Bank. Borrower acknowledges that the failure to take such actions and to
deliver such documents, instruments, agreements and certificates by such date, shall be an Event of Default hereunder.” 

  
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 6. Representations and Warranties. To induce Bank to enter into this
Agreement, Borrower and each other Obligor hereby represents and warrants to Bank as follows: 

(a) All representations and warranties contained in this Agreement and in any and all of the other
Loan Documents are and remain true, correct and complete as of the date of this Agreement (except to the extent such representations and warranties expressly refer to an earlier date, in which case, they are and remain true, correct and complete as
of such earlier date), and all such representations and warranties shall survive the execution of this Agreement. 
 (b) The execution, delivery and performance by Borrower and each other Obligor of this Agreement and all documents contemplated hereunder are within Borrower’s and such other Obligor’s
powers, have been duly authorized, and are not in conflict with Borrower’s or any other Obligor’s certificate of incorporation, by-laws or operating agreement, or the terms of any charter or other organizational document of Borrower or
such other Obligor; and all such documents constitute valid and binding obligations of Borrower and each such other Obligor, enforceable in accordance with their terms. In addition, such execution, delivery and performance by Borrower and each other
Obligor will not violate any law, rule or order of any court or governmental agency or body to which Borrower or any other Obligor is subject; and cannot (except as expressly provided or contemplated herein) result in the creation or imposition of
any lien, security interest or encumbrance on any now owned or hereafter acquired property of Borrower. 
 (c) No event has occurred or failed to occur that is, or, with notice or lapse of time or both would constitute a default, an Event of Default, or a breach or failure of any condition under any
Loan Document. Borrower and each other Obligor, taken as a whole, are Solvent. 
 (d) As
of the date hereof, (i) Borrower has no Material Subsidiaries, or Subsidiaries that are required to be designated as Material Subsidiaries under the Loan Documents, other than Closing Date Guarantor and PBS; and (ii) PBS is not a 5%
Subsidiary. 
 (e) Attached hereto as Schedule A is a true, correct and
complete list of all contracts, instruments, leases and other agreements to which Borrower or any of its Subsidiaries are a party or by which any of them or their assets or properties are bound as of the date hereof (i) that are material to
Borrower or to Borrower and its Subsidiaries, taken as a whole, or (ii) the breach, cancellation or termination of which, or default under, could reasonably be expected to have a Material Adverse Effect. 

(f) The Revolving Loan represents an unconditional, absolute, valid and enforceable obligation
against Borrower and the Guaranties represent unconditional, absolute, valid and enforceable obligations of each other Obligor. Neither Borrower nor any other Obligor has any claims, counterclaims, or defenses against Bank or any other person or
entity which would or might affect: (i) the enforceability of any provisions of the Loan Documents; or (ii) the collectability of sums advanced by Bank in connection with the Revolving Loan. Neither Borrower nor any other Obligor has any
offsets, disputes or disagreements of any kind or nature whatsoever with respect to its obligations under the Loan Documents. Borrower and each other Obligor understands and acknowledges that Bank is entering into this Agreement in reliance upon,
and in partial consideration for, these acknowledgments and representations, and agrees that such reliance is reasonable and appropriate. 

  
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 7. Confirmation of Guaranty. Each Guarantor ratifies and
reaffirms its obligations under the Guaranty, including the MHM Guaranty, that it has provided to Bank, and each and every term, condition, and provision of such Guaranty, the Security Agreement and each other Loan Document to which it is a party.
Each Guarantor further represents and warrants that it has no defenses or claims against Bank that would or might affect the enforceability of its Guaranty or any other Loan Document and that its Guaranty and each other Loan Document to which it is
a party remain in full force and effect. 
 8. Release. Borrower and each Guarantor hereby, for
itself, its successors, heirs, executors, administrators and assigns (each a “Releasing Party” and collectively, the “Releasing Parties”), releases, acquits and forever discharges Bank, its directors, officers,
employees, agents, attorneys, affiliates, successors, administrators and assigns (“Released Parties”) of and from any and all claims, actions, causes of action, demands, rights, damages, costs, loss of service, expenses and
compensation whatsoever which any Releasing Party might have because of anything done, omitted to be done, or allowed to be done by any of the Released Parties and in any way arising out of or connected with the Revolving Loan or this Agreement or
the other Loan Documents as of the date of execution of this Agreement, WHETHER KNOWN OR UNKNOWN, FORESEEN OR UNFORESEEN, including, without limitation, any specific claim raised by any Releasing Party, (the “Released Matters”).
Releasing Parties each further agrees never to commence, aid or participate in (except to the extent required by order or legal process issued by a court or governmental agency of competent jurisdiction) any legal action or other proceeding based in
whole or in part upon the Released Matters. In furtherance of this general release, Releasing Parties each acknowledges and waives the benefits of California Civil Code Section 1542 (and all similar ordinances and statutory, regulatory, or
judicially created laws or rules of any other jurisdiction), which provides: 
 A GENERAL RELEASE DOES NOT EXTEND
TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR SUSPECT TO EXIST IN HIS OR HER FAVOR AT THE TIME OF EXECUTING THE RELEASE, WHICH IF KNOWN BY HIM OR HER MUST HAVE MATERIALLY AFFECTED HIS OR HER SETTLEMENT WITH THE DEBTOR. 

Releasing Parties each agree that this waiver and release is an essential and material term of this Agreement and that the agreements in
this paragraph are intended to be in full satisfaction of any alleged injuries or damages in connection with the Released Matters. Releasing Parties each represent and warrant that it has not purported to convey, transfer or assign any right, title
or interest in any Released Matter to any other person or entity and that the foregoing constitutes a full and complete release of the Released Matters. Releasing Parties each also understands that this release shall apply to all unknown or
unanticipated results of the transactions and occurrences described above, as well as those known and anticipated. Releasing Parties each has consulted with legal counsel prior to signing this release, or had an opportunity to obtain such counsel
and knowingly chose not to do so, and executes such release voluntarily, with the intention of fully and finally extinguishing all Released Matters. Notwithstanding anything in this Agreement, Borrower does not waive any of Bank’s obligations
under the terms of the Loan Agreement as amended by this Agreement. 
 9. Dispute Resolution. This
Agreement hereby incorporates any alternative dispute resolution agreement previously, concurrently or hereafter executed between Borrower or any Guarantor, and Bank. 

  
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 10. Miscellaneous. 

(a) All the parties hereto agree to and will cooperate fully with each other in the performance of
this Agreement and the Loan Documents including, without limitation, executing any additional documents and instruments reasonable or necessary to the full performance of this Agreement. Without limiting the generality of the foregoing, Borrower
agrees to execute such other and further documents and instruments as Bank may request to implement the provisions of this Agreement. 
 (b) This Agreement shall be binding upon and inure to the benefit of and be enforceable by the parties hereto, and their respective successors and assigns. No other person or entity shall be
entitled to claim any right or benefit hereunder, including, without limitation, the status of a third party beneficiary hereunder. 
 (c) Bank and Borrower agree that except as expressly provided herein, the Loan Documents shall remain in full force and effect in accordance with their respective terms, and this Agreement shall
not be construed to: 
 (i) Waive or impair any rights, powers or remedies of Bank under the Loan
Documents; 
 (ii) Constitute an agreement by Bank or require Bank to grant forbearance periods or extend
the term of any credit extended by Bank or the time for payment of any of Borrower’s obligations to Bank except as expressly provided herein, none of which Bank agrees or has agreed to do, and all of which matters are in Bank’s sole and
absolute discretion; 
 (iii) Make any other loans or other extension of credit to Borrower or any
Guarantor; 
 (iv) Imply a willingness on the part of Bank to grant any similar or other future waivers,
consents, amendments or modifications to any of the terms and conditions of the Loan Agreement or the other Loan Documents or grant any waivers or consents, or shall in any way prejudice, impair or effect any rights or remedies of the Bank under the
Loan Agreement or the other Loan Documents; 
 (v) Operate as a waiver of, or as an amendment of, any
right, power, or remedy of Bank under the Loan Agreement, as in effect prior to the date hereof; or 

(vi) Constitute a satisfaction of Borrower’s or any Guarantor’s Obligations. 

(d) In the event of any inconsistency between the terms of this Agreement and any other Loan
Document, this Agreement shall govern. Each Obligor acknowledges that it has consulted with counsel and with such other experts and advisors as it has deemed necessary in connection with the negotiation, execution and delivery of this Agreement, or
has had an opportunity to so consult and has knowingly chosen not to do so. This Agreement shall be construed without regard to any presumption or rule requiring that it be construed against the party causing this

  
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Agreement or any part hereof to be drafted. The headings used in this Agreement are for convenience only and shall be disregarded in interpreting the substantive provisions of this Agreement.

 (e) This Agreement and the other Loan Documents shall not be deemed or construed to
create a partnership, tenancy in common, joint tenancy, joint venture, co-ownership or any other relationship aside from a continuing debtor-creditor relationship between Borrower, on the one hand, and Bank, on the other. 

(f) in case any provision in this Agreement shall be invalid, illegal or unenforceable, such
provision shall be severable from the remainder of this Agreement and the validity, legality and enforceability of the remaining provisions shall not in any way be affected or impaired thereby. 

(g) If Bank receives any payments or rents, issues, profits or proceeds of any collateral which are
subsequently invalidated, declared to be fraudulent or preferential, set aside or required to be paid to a trustee, debtor-in-possession, receiver or any other party under any bankruptcy law, common law, equitable cause or otherwise, then, to such
extent, the obligations or part thereof intended to be satisfied by such payments or proceeds shall be reversed and continue as if such payments or proceeds had not been received by Bank. 

(h) Notwithstanding the rights given to any Obligor pursuant to California Civil Code sections 1479
and 2822 (and any amendments or successors thereto), to designate how payments will be applied, each Obligor hereby waives such rights and Bank shall have the right in its sole discretion to determine the order and method of the application of
payments to this and/or any other credit facilities that may be provided by Bank to any Obligor and to revise such application prospectively or retroactively at its discretion. 

(i) This Agreement may not be amended, waived or modified in any manner without the prior written
consent of Bank and Borrower. 
 (j) Borrower shall reimburse Bank for all costs and
expenses, including, without limitation, reasonable attorneys’ fees and disbursements (and fees and disbursements of Bank’s in-house legal counsel and staff) expended or incurred by Bank in any arbitration, mediation, judicial reference,
legal action or otherwise in connection with: (i) the negotiation, preparation, amendment, interpretation and enforcement of the Loan Documents, including, without limitation, during any workout, attempted workout, and/or in connection with the
rendering of legal advice as to Bank’s rights, remedies and obligations under the Loan Documents; (ii) collecting any sum which becomes due Bank under any Loan Document; (iii) any proceeding for declaratory relief, any counterclaim to
any proceeding, or any appeal; or (iv) the protection, preservation or enforcement of any rights of Bank. For purposes of this section, attorneys’ fees shall include, without limitation, fees incurred in connection with the following:
(1) contempt proceedings; (2) discovery; (3) any motion, proceeding or other activity of any kind in connection with a bankruptcy proceeding or case arising out of or relating to any petition under Title 11 of the United States
Code, as the same shall be in effect from time to time, or any similar law; (4) garnishment, levy, and debtor and third party examinations; and (5) postjudgment motions and proceedings of any kind, including, without limitation, any
activity taken to collect or enforce any judgment. All of such costs and expenses shall bear interest from the time of demand at the rate then in effect under the Loan Agreement. 

  
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 (k) This Agreement and all other Loan Documents and
the rights and obligations of the parties hereto shall be governed by the laws of the State of California without regard to principles concerning choice of law. 

(l) This Agreement may be executed by facsimile signature and in any number of counterparts which,
when taken together, shall constitute but one agreement. 
 (m) This Agreement and the
other Loan Documents are intended by the parties as the final expression of their agreement and therefore incorporate of negotiations of the parties hereto and are the entire agreement of the parties hereto. Borrower acknowledges that it is relying
on no written or oral agreement, representation, warranty, or understanding of any kind made by Bank or any employee or agent of Bank except for the agreements of Bank set forth herein or in the other Loan Documents. Except as expressly set forth in
this Agreement, the other Loan Documents remain unchanged and in full force and effect. 

(n) Bank is subject to the USA Patriot Act and hereby notifies each Obligor that pursuant to the
requirements of that Act, Bank is required to obtain, verify and record information that identifies Borrower, which information includes the name and address of each Obligor and other information that will allow Bank to identify Obligors in
accordance with that Act. 
 [Remainder of Page Left Blank] 

  
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 IN WITNESS WHEREOF, Bank, Borrower and Closing Date Guarantor have
executed this Agreement as of the date set forth in the preamble. 
  

									
	 BORROWER
	 		 	 BANK

			
	 WAGEWORKS, INC.
	 		 	 UNION BANK, N.A.

					
	 By:
	 	 /s/ Kim Jackson
	 		 	 By:
	 	  

	 Name: Kim Jackson
	 		 	 Name: James B. Goudy

	 Title: General Counsel and Secretary
	 		 	 Title: Vice President

				
	 GUARANTOR
	 		 		 	
				
	 MHM RESOURCES, LLC
	 		 		 	
					
	 By:
	 	 /s/ Kim Jackson
	 		 		 	
	 Name: Kim Jackson
	 		 		 	
	 Title: Secretary
	 		 		 	

 IN WITNESS WHEREOF, Bank, Borrower and Closing Date Guarantor have
executed this Agreement as of the date set forth in the preamble. 
  

									
	 BORROWER
	 		 	 BANK

			
	 WAGEWORKS, INC.
	 		 	 UNION BANK, N.A.

					
	 By:
	 	  
	 		 	 By:
	 	 /s/ James B. Goudy

	 Name:
	 	  
	 		 	 Name: James B. Goudy

	 Title:
	 	  
	 		 	 Title: Vice President

				
	 GUARANTOR
	 		 		 	
				
	 MHM RESOURCES, LLC
	 		 		 	
					
	 By:
	 	  
	 		 		 	
	 Name:
	 	  
	 		 		 	
	 Title:
	 	  
	 		 		 	

 SCHEDULE A 
 Material Agreements 
 1. Amended and Restated Investors’ Rights
Agreement, dated as of December 22, 2005, between Borrower and certain holders of Borrower’s capital stock named therein, as amended by Amendment No. 1 to Amended and Restated Investors’ Rights Agreement, dated as of
December 28, 2009, between Borrower and certain holders of Borrower’s capital stock named therein, and as further amended by Amendment No. 2 to Amended and Restated Investors’ Rights Agreement, dated as of July 30, 2010,
between Borrower and certain holders of Borrower’s capital stock named therein. 
 2. Warrant Agreement to Purchase Shares
of Series C Preferred Stock, dated as of May 23, 2005, by and between Borrower and Hercules Technology Growth Capital, Inc. 
 3. Warrant to Purchase Common Stock of Borrower, issued to ORIX Venture Finance LLC, dated September 26, 2007. 
 4. Second Amended and Restated Employment Agreement, dated as of November 23, 2010, between Borrower and Joseph L. Jackson. 
 5. Sublease Agreement between Oracle USA, Inc. and Borrower, dated as of September 13, 2006, as amended by First Amendment to Sublease between Oracle USA, Inc. and Borrower, dated as of
October 30, 2006, and as further amended by Second Amendment to Sublease between Oracle America, Inc. and Borrower, dated as of May 1, 2011. 
 6. Commercial Building Lease, by and between Applied Buildings, LLC and Borrower, dated as of December 17, 2004, as assigned to Borrower pursuant to Assignment and Assumption of Lease, between, HCAP
Strategies, Inc. and Borrower, dated as of May 16, 2005 and as amended by Amendment to Commercial Building Lease, between Applied Buildings, LLC and Borrower, dated as of September 8, 2005. 

7. Lease, by and between Phoenix Investors #25, L.L.C. and Borrower, dated as of July 23, 2007, as amended by First Amendment to
Lease, by and between Phoenix Investors #25, L.L.C. and Borrower, dated as of May 24, 2010, and as further amended by Second Amendment to Lease, by and between Phoenix Investors #25, L.L.C. and Borrower, dated as of August 31, 2010.

 8. Sublease Agreement, dated as of June 1, 2011, by and between Borrower and FBMC Benefits Management, Inc. 

9. Pinnacle Corporate Centre IV Standard Office Lease, dated as of February 8, 2008, by and between BK Pinnacle IV LLC and MHM, as
amended by First Amendment to Lease, dated as of April 30, 2008, by and between BK Pinnacle IV LLC and MHM, and as further amended by Second Amendment to Lease dated as of August 12, 2008 by and between BK Pinnacle IV LLC and MHM.EX-10.21

 Exhibit 10.21 
 AMENDMENT NO. 1, dated as of March 1, 2012 (this “Amendment”), to that certain Credit Agreement, dated as of August 29, 2011 (as further amended, supplemented, amended
and restated, waived or otherwise modified from time to time, the “Credit Agreement”), among RAILAMERICA, INC., a Delaware corporation (“RailAmerica”); RAILAMERICA TRANSPORTATION CORP., a Delaware corporation
(“RATC,” together with RailAmerica, the “Borrowers” and each individually, a “Borrower”); the lenders party thereto from time to time (the “Lenders”), the LETTER OF CREDIT ISSUER
party thereto from time to time; CITIBANK, N.A., as administrative agent (in such capacity, the “Administrative Agent”) and as collateral agent (in such capacity, the “Collateral Agent”) for the Lenders; and
CITIGROUP GLOBAL MARKETS INC. (“CGMI”), as sole lead arranger and sole bookrunner (in such capacity, the “Lead Arranger”). Capitalized terms used and not otherwise defined herein shall have the meanings assigned to
them in the Credit Agreement (as amended hereby). 
 WHEREAS, pursuant to subsection 13.1 of the Credit Agreement the
Administrative Agent and the Credit Parties may, with the consent of the Required Lenders, amend and supplement the Credit Agreement. 
 NOW, THEREFORE, in consideration of the premises contained herein and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto, intending
to be legally bound hereby, agree as follows: 
 Section 1. Amendments to the Credit Agreement. The Credit
Agreement is hereby amended effective as of the date hereof as follows: 
 (a) Section 1.1 of the Credit
Agreement is hereby amended by adding the following definitions: 
 (i) “Amendment No. 1”
means Amendment No. 1 to this Agreement, dated as of March 1, 2012. 
 (ii) “Amendment
No. 1 Effective Date” means March 1, 2012. 
 (iii) “Consolidated Senior Secured Net
Debt” shall mean, as of any date of determination (x) the aggregate principal amount of all Indebtedness of RailAmerica and the Restricted Subsidiaries determined on a consolidated basis in accordance with GAAP that is secured by a
Lien minus (y) the lesser of (A) $50,000,000 and (B) the amount of cash and Permitted Investments included on the balance sheet of RailAmerica and its Restricted Subsidiaries on such date other than cash and Permitted
Investments (i) constituting proceeds of a Borrowing hereunder or any Term Loans, in each case borrowed at the time of determination; (ii) designated as or representing proceeds from any Excluded Contribution or Specified Equity
Contribution; (iii) held by Restricted Subsidiaries that is contractually restricted from being distributed to the Borrowers; and (iv) that are subject to a Lien (other than Liens permitted under clauses (a) and (k) of the
definition of Permitted Liens and Section 10.2(a)). 
 (iv) “Consolidated Senior Secured Net Debt to
Consolidated EBITDA Ratio” shall mean, as of any date of determination, the ratio of (a) Consolidated Senior Secured Net Debt as of the last day of the most recent Test Period to (b) Consolidated EBITDA

 
for such Test Period (which for such purposes of Section 10.9 shall exclude amounts earned from, or received from the assignment of, the tax credit available under Section 45G of the
Code); provided that the Consolidated Senior Secured Net Debt to Consolidated EBITDA Ratio shall be calculated on a Pro Forma Basis. 
 (v) “Existing Lenders” shall have the meaning provided in Section 2.15. 
 (vi) “Junior Financing” shall mean (i) any Indebtedness that is subordinated in right of payment to any of the Obligations or (ii) any Indebtedness incurred or outstanding
pursuant to Section 10.1(i), (k) or (m) that is either not secured or secured by a Lien on any Collateral that is junior to the Lien on such Collateral securing the Obligations. 

(vii) “Junior Lien Priority” shall have the meaning provided in the Intercreditor Agreement. 

(viii) “New Commitment” shall have the meaning provided in Section 2.15. 

(ix) “New Lender” shall have the meaning provided in Section 2.15. 

(x) “Notice of Borrowing/Continuation” shall mean a notice substantially in the form of Exhibit N (or
such other form as may be acceptable to the Administrative Agent). 
 (xi) “Other Pari Passu Lien
Obligations” has the meaning assigned to such term in the Intercreditor Agreement. 
 (xii)
“Specified Entity” shall mean an entity set forth on Schedule 1.1(c) or Schedule 1.1(d). 

(xiii) “Specified Equity Contribution” shall have the meaning provided in Section 10.9. 

(xiv) “Tender Offer” shall mean the tender offer for $444,000,000 in principal amount of the Secured
Notes pursuant to the Offer to Purchase and related documents dated February 1, 2012. 
 (xv) “Term
Loan Agent” shall have the meaning provided in the definition of Term Loan Credit Agreement. 
 (xvi)
“Term Loan Credit Agreement” shall mean that credit agreement dated as of the Amendment No. 1 Effective Date by and among the Borrowers, the lenders party thereto from time to time, Morgan Stanley Senior Funding, Inc. as
administrative agent (in such capacities, the “Term Loan Agent”), and the other agents and arrangers party thereto, as amended, supplemented, amended and restated, waived or otherwise modified from time to time. 

  
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 (xvii) “Term Loan Facility Indebtedness” shall mean all
Indebtedness of the Credit Parties outstanding under the Term Loan Credit Agreement. 
 (xviii) “Term
Loan Security Documents” shall have the meaning provided in the Intercreditor Agreement. 
 (xix)
“Term Loans” shall mean the “Loans” as defined in the Term Loan Credit Agreement. 
 (b) Each of the
following definitions in Section 1.1 of the Credit Agreement shall be amended and restated in their entirety as follows: 
 (i) “ABR Loan” shall mean any Loan bearing interest at a rate determined by reference to the ABR and, in any event, shall include all Swingline Loans. 

(ii) “Commitment” shall mean (a) with respect to each Lender that is a Lender on the Amendment No.1
Effective Date, the amount set forth opposite such Lender’s name on Schedule 1.1(b) as such Lender’s “Commitment”, (b) in the case of any New Lender that becomes a Lender under Section 2.15, the amount specified
as such Lender’s “New Commitment” in the Joinder Agreement pursuant to which such New Lender assumed a portion of the Total Commitment and (c) in the case of any Lender that becomes a Lender after the Amendment No.1 Effective
Date, the amount specified as such Lender’s “Commitment” in the Assignment and Acceptance pursuant to which such Lender assumed a portion of the Total Commitment, in each case as the same may be changed from time to time pursuant to
terms hereof. The aggregate amount of the Commitments as of the Amendment No.1 Effective Date is $100.0 million. 

(iii) “Credit Documents” shall mean Amendment No. 1, this Agreement, the Guarantee, the Security
Documents, each Letter of Credit, any promissory notes issued by the Borrowers hereunder and the Fee Letters. 

(iv) “Excluded Entity” means any Restricted Subsidiary (other than RATC) that RailAmerica has designated
as such in an Officers’ Certificate delivered to the Administrative Agent on or before the Closing Date; provided that (x) no such Restricted Subsidiary (other than the Specified Entity listed on Schedule 1.1(d)) shall hold or
obtain any assets (other than Equity Interests in another Restricted Subsidiary that would also qualify as an Excluded Entity) and (y) each such Restricted Subsidiary (other than the Specified Entities listed on either Schedule 1.1(c) or
1.1(d)) shall be intended to be dissolved within six months after the Closing Date. 
 (v) “Intercreditor
Agreement” shall mean the Intercreditor Agreement, dated as of June 23, 2009, as amended and restated on the Closing Date and the Amendment No. 1 Effective Date, among the Administrative Agent, the Collateral Agent, U.S. Bank,
National Association, in its capacity as trustee for the Secured Notes and “Notes Collateral Agent” (referred to herein as “Fixed Asset Collateral Agent”), and the Term Loan Agent, as the same may be further amended or
supplemented or otherwise modified from time to time in accordance with the terms hereof and thereof. 

  
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 (vi) “Joinder Agreement” shall mean an agreement
substantially in the form of Exhibit B to Amendment No. 1. 
 (vii) “Mortgage” shall mean
an agreement, including, but not limited to, a mortgage, deed of trust or any other document, creating and evidencing a Lien on Mortgaged Property, with such schedules and including such provisions as shall be necessary to conform such document to
applicable local law or as shall be customary under applicable local law, in each case as the same may be amended, amended and restated, supplemented, assigned or otherwise modified from time to time. 

(viii) “Mortgaged Property” shall mean (a) each real property identified as a Mortgaged Property on
Schedule 7(a) to the Perfection Certificate dated the Closing Date and (b) each real property, if any, which shall be subject to a Mortgage delivered after the Closing Date pursuant to Sections 9.10, 9.13 or 9.17. For the avoidance of
doubt, in no case and at no time shall Mortgaged Property include any Buildings or Manufactured (Mobile) Homes. 

(ix) “Permitted Acquisition” shall mean any transaction for the (a) acquisition of all or
substantially all of the property of any Person or of any business or division of any Person by RailAmerica or a Restricted Subsidiary; or (b) acquisition (including by merger or consolidation) of all of the Equity Interests of any Person by
RailAmerica or a Restricted Subsidiary; provided that each of the following conditions shall be met: 

(a) such acquisition and all transactions related thereto shall be consummated in accordance with applicable law;

 (b) in the case of the acquisition of Equity Interests, (i) no less than 50.1% of all of the Equity
Interests acquired or otherwise issued by such Person or any newly formed Subsidiary of a Borrower in connection with such acquisition shall be owned by a Borrower or a Subsidiary Guarantor thereof, (ii) such Person or any newly formed
Subsidiary shall become a Restricted Subsidiary and (iii) with respect to any Person or newly formed or acquired Subsidiary that is a Wholly-Owned Subsidiary of a Borrower or a Subsidiary Guarantor, such Borrower or such Subsidiary Guarantor
shall have taken, or shall cause to be taken, such actions necessary for such newly formed or acquired Wholly-Owned Subsidiary to become a Subsidiary Guarantor as set forth in Section 9.10; provided that in the case of an acquisition of
the Equity Interests of a Person pursuant to this clause (b) that does not become a Credit Party, such acquisition shall only be made to the extent capacity for Investments in Subsidiaries that are not Guarantors under Section 10.5 exists
(and shall reduce such capacity); 

  
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 (c) in the case of an acquisition of assets, such assets shall be held,
after giving effect to such acquisition, by a Borrower or a Subsidiary Guarantor or, to the extent there is capacity for Investments in Subsidiaries that are not Guarantors under Section 10.5, any other Restricted Subsidiary that is not a
Subsidiary Guarantor (which Investment will reduce such capacity); 
 (d) such acquisition shall result in the
Collateral Agents, for the benefit of the applicable Lenders, being granted a security interest in any assets so acquired by a Borrower or Subsidiary Guarantor to the extent required by Section 9.10 or 9.12 (it being agreed that, in the case of
an acquisition of Equity Interests, a Borrower or the applicable Subsidiary Guarantor shall only pledge such Equity Interests that are owned by such Borrower or Subsidiary Guarantor); 

(e) the Person or business to be acquired shall be, or shall be engaged in, a business of the type that RailAmerica and
the Restricted Subsidiaries are permitted to be engaged in under Section 10.12; and 
 (f) no Default or
Event of Default shall have occurred and be continuing or would result therefrom. 
 (x) “Secured
Notes” shall mean RailAmerica’s 9.25% Senior Secured Notes due 2017. 
 (xi) “Secured Notes
Indenture” shall mean the Indenture dated as of June 23, 2009, among RailAmerica, the guarantors party thereto and U.S. Bank National Association, as trustee, pursuant to which the Secured Notes are issued, as in effect on the Closing
Date or as amended solely to add additional guarantors thereto. 
 (xii) “Security Documents”
shall mean, collectively, (a) the Security Agreements, (b) the Intercreditor Agreement, (c) the Mortgages, (d) the Closing Date Fixed Asset Security Agreement Affirmation and (e) each other security agreement or instrument
or document executed and delivered pursuant to Sections 9.10. 9.12 or 9.17 or pursuant to any of the Security Agreements to secure any of the Obligations (for the avoidance of doubt, the Security Documents shall include, but not be limited to, the
Fixed Asset Security Documents). 
 (xiii) “Subsidiary Guarantors” shall mean (a) each
Domestic Subsidiary (other than an Excluded Entity) on the Closing Date and (b) each Restricted Domestic Subsidiary that becomes a party to the Guarantee after the Closing Date pursuant to Section 9.10; provided that if an Excluded
Entity (other than the Specified Entities listed on Schedules 1.1(c) or 1.1(d)) is not dissolved on or before the six-month anniversary of the Amendment No. 1 Effective Date, such Excluded Entity (other than any Specified Entity listed on
Schedule 1.1(c) or 1.1(d)) shall promptly become a Subsidiary Guarantor, but in any event within ten Business Days after such six-month anniversary. 

  
 -5-

 (c) The definitions of the following terms in Section 1.1 of the Credit Agreement shall
be amended as follows: 
 (i) “Available Amount Basket” shall be amended by (i) deleting
the “or” before clause (d) in the proviso of clause (2) thereof and replacing it with a “,”, (ii) adding the following at the end of the proviso of clause (2) thereof: “or (e) Specified Equity
Contributions”, (iii) adding the words “or Specified Equity Contributions” at the end of the second parenthetical in clause (3) thereof; 

(ii) “Change of Control” shall be amended by adding “, the Term Loan Credit Agreement or any
Permitted Refinancing Indebtedness in respect thereof” after the words “the Secured Notes or any Permitted Refinancing Indebtedness in respect thereof”; 

(iii) “Collateral” shall be amended by changing the reference from “Section 9.10 or 9.12” to
“Section 9.10, 9.12 or 9.15(B)”. 
 (iv) “Collateral Agent” shall be amended by
replacing the words “collateral agent” in clause (b) thereof with the words “Authorized Representative”. 
 (v) “Commitment Fee Rate” shall be amended by (i) deleting the words “and (iii) prior to the first Adjustment Date” and (ii) by replacing the “,” before
“(ii) with the word “and”; 
 (vi) “Consolidated Interest Expense” shall be
amended by adding the words “(i) any acceleration of the amortization of original issue discount resulting from the Tender Offer and (ii)” immediately after the words “but excluding”; 

(vii) “Consolidated Senior Secured Debt to Consolidated EBITDA Ratio” shall be amended by deleting the
parenthetical “(which for such purposes of Section 10.9 shall exclude amounts earned from, or received from the assignment of, the tax credits available under Section 45G of the Code)”; 

(viii) “Designated Preferred Stock” shall be amended by deleting the first parenthetical and replacing it
with “(other than Disqualified Capital Stock and other than to the extent issued in connection with a Specified Equity Contribution)”; 
 (ix) “Excluded Contribution” shall be amended by adding the words “or in connection with a Specified Equity Contribution” at the end of the second parenthetical in clause
(b) thereof. 
 (x) “Fixed Asset Collateral Agent” shall be amended by deleting the proviso
thereto; 
 (xi) “Fixed Charge Coverage Ratio” shall be amended by adding the words “during
such Test Period” immediately prior to the words “and (iii)”; 

  
 -6-

 (xii) “Management Group” shall be amended by adding the
words “, Senior Vice President” immediately after the words “Executive Vice President”; 

(i) “Net Proceeds” shall be amended by replacing the two references in such definition to “the
Company” with “RailAmerica or a Restricted Subsidiary”. 
 (ii) “Permitted Collateral
Liens” shall be amended by adding a comma in between the references to clauses (g) and (j). 

(iii) “Permitted Refinancing Indebtedness” shall be amended by (I) replacing the parenthetical in
clause (a) thereof with the following: “(except by the amount of any accrued and unpaid interest thereon and by the amount of any fees and expenses payable including any premiums and make whole or prepayment premiums paid in connection
with such refinancing)” and (II) replacing clause (z) thereof in its entirety with the following: “does not have any mandatory redemption, mandatory offer to purchase or sinking fund obligation (other than (i) customary offers to
purchase or prepayment events upon a change of control, asset sale or event of loss, (ii) other prepayment or redemption events not more onerous to RailAmerica and its Restricted Subsidiaries than those set forth in Section 5.2 of the Term
Loan Credit Agreement as in effect on the Amendment No. 1 Effective Date and (iii) customary acceleration rights after an event of default) at a date that is earlier than any mandatory redemption, mandatory offer to purchase or sinking
fund obligation in the Initial Indebtedness”; 
 (iv) “Pro Forma Adjustment Certificate”
shall be amended by deleting the words “or setting forth the information described in clause (iv) to Section 9.1(d)”; 
 (v) “Pro Forma Basis” shall be amended by adding the words “(and as if such incurrence and repayment remains in effect on the Determination Date)” at the end of clause
(C) thereof; 
 (vi) “Secured Hedge Agreement” shall be amended by adding the words
“not prohibited hereunder” immediately after the words “any Hedge Agreement”; and 
 (vii)
“Unrestricted Subsidiary” shall be amended by (A) adding the words “RATC or” after the words “other than” in clause (b) thereof and (B) adding the words “, the Term Loan Facility Indebtedness
or any Permitted Refinancing Indebtedness in respect thereof” after the words “the Secured Notes or any Permitted Refinancing Indebtedness in respect thereof”. 
 (d) Section 1.1 of the Credit Agreement shall be amended by deleting the definitions of “Consolidated First Lien Secured Debt”, “Consolidated First Lien Secured Debt to Consolidated
EBITDA Ratio”, “Increased Amount Date”, “New Commitments”; “New Lender”; “Notice of Borrowing”; “Notice of Conversion or Continuation”; “Regulation Z” and “Specified Financial
Maintenance Covenant” in their entirety. 

  
 -7-

 (e) The Credit Agreement shall be amended by replacing the words “Notice of
Borrowing” or “Notice of Borrowing or Notice of Conversion or Continuation” or “Notice of Conversion or Continuation”, in each case, with the words “Notice of Borrowing/Continuation” each time such words appear in
the Credit Agreement. 
 (f) Section 2.2 of the Credit Agreement shall be amended by deleting the word “five” and
replacing it with the word “seven.” 
 (g) Section 2.3 of the Credit Agreement shall be amended by replacing the
words “(each such notice, a “Notice of Borrowing”)” with the words “pursuant to a Notice of Borrowing/Continuation”. 
 (h) Section 2.6 of the Credit Agreement shall be amended by replacing the words (“each, a “Notice of Conversion or Continuation”) with the words “pursuant to a Notice of
Borrowing/Continuation”. 
 (i) Section 2.15 of the Credit Agreement shall be replaced in its entirety with the
following: 
 “2.15. Commitment Increase. On the Amendment No. 1 Effective Date, the aggregate
Commitments shall be increased from $75,000,000 to $100,000,000, and Schedule 1.1(b) shall be deemed to be replaced in its entirety with Schedule 1.1(b) to Amendment No. 1. On the Amendment No. 1 Effective Date (a) each Person that is
an eligible assignee pursuant to Section 13.6(b) and is obtaining a new Commitment (each, a “New Commitment”) on the Amendment No. 1 Effective Date shall execute and deliver a Joinder Agreement to the Administrative
Agent (each such Person, a “New Lender”), and each of the New Lenders shall purchase from each of the Lenders with Commitments immediately prior to the Amendment No. 1 Effective Date (the “Existing Lenders”),
at the principal amount thereof (together with accrued interest), such interests in the Revolving Credit Loans outstanding on the Amendment No. 1 Effective Date as shall be necessary in order that, after giving effect to all such assignments
and purchases, such Revolving Credit Loans will be held by Existing Lenders and New Lenders ratably in accordance with their respective Commitments after giving effect to such increase to the Commitments on the Amendment No. 1 Effective Date
pursuant to Amendment No. 1, (b) each New Commitment shall be deemed for all purposes a Commitment and each Loan made thereunder shall be deemed, for all purposes, a Revolving Credit Loan and (c) each New Lender shall become a Lender
with respect to the New Commitments and all matters relating thereto. In addition, on the Amendment No. 1 Effective Date, each of the New Lenders shall have been deemed to purchase from each of the Existing Lenders, at the face amount thereof,
such of the L/C Participations outstanding on the Amendment No. 1 Effective Date as shall be necessary in order that, after giving effect to all such purchases, the L/C Participations will be held by Existing Lenders and New Lenders ratably in
accordance with their respective 

  
 -8-

 
Commitments after giving effect to such increase to the Commitments on the Amendment No. 1 Effective Date, and in such capacity, the New Lenders shall become L/C Participants (it being
understood that any Letter of Credit Fees accrued for the account of Existing Lenders for periods prior to the Amendment No. 1 Effective Date shall not be reallocated or otherwise shared with the New Lenders in their capacity as such).”

 (j) Section 5.1 of the Credit Agreement shall be amended by adding the following sentence at the end of such clause:
“Each prepayment in respect of any Revolving Credit Loans pursuant to this Section 5.1 shall be applied on a pro rata among such Revolving Credit Loans of each Lender in accordance with their respective Applicable Percentages.”

 (k) Section 5.2 of the Credit Agreement shall be amended by (i) replacing the words “Section 5.2(a) or
(d)” with the words “Section 5.2(a), (d) or (e)” in clause (b) thereof and (ii) adding the following as a new clause (e): 
 “(e) Specified Equity Contribution. On the date that Rail America receives a Specified Equity Contribution, the Borrowers shall make prepayments of Loans in an aggregate amount equal to 100%
of such Specified Equity Contribution; provided that no prepayments of Loans shall be required pursuant to this Section 5.2(e) except to the extent of, and not to exceed, the amount of Specified Equity Contribution required to be applied
toward such prepayment after any required payment of the obligations under the Term Loan Credit Agreement (it being understood that amounts actually applied toward prepayment of the obligations under the Term Loan Credit Agreement shall reduce the
amount required to be applied toward prepayments hereunder).” 
 (l) Section 6.2 of the Credit Agreement shall be
amended by replacing the words “closing date” with “Closing Date” 
 (m) Section 8.3 of the Credit
Agreement shall be amended by (A) changing the reference to “Secured Note Indenture” to “Secured Notes Indenture”, (B) adding a “)” immediately after the term “Secured Notes Indenture”,
(C) adding the words “(including the Term Loan Credit Agreement)” immediately after the words “any loan agreement” and (D) removing the “)” following the word “bound”. 

(n) Section 8.12(a) of the Credit Agreement shall be amended by adding the following immediately at the end of such clause: “No
Excluded Entity (other than the Specified Entity set forth on Schedule 1.1(d)) holds any assets other than Equity Interests in another Excluded Entity.” 
 (o) Section 8.14(b) of the Credit Agreement shall be amended by deleting the words “, stored, transported”. 

  
 -9-

 (p) Section 9.1 of the Credit Agreement shall be amended by (i) replacing the
words “RailAmerica will furnish to each Lender and the Administrative Agent” with the words “RailAmerica will furnish to the Administrative Agent”; (ii) deleting clause (1) of clause (d) thereof in its entirety;
(iii) replacing the reference to the word “the Company” in clause (d) thereof to “RailAmerica”; (iv) replacing the words “Consolidated Senior Secured Debt to Consolidated EBITDA Ratio” with
“Consolidated Senior Secured Net Debt to Consolidated EBITDA Ratio” in clause (d) thereof; (v) deleting the word “Initial” from clause (h) thereof; and (vi) adding the following new clauses (k) and (l):

 “(k) Documents required to be delivered pursuant to Section 9.1(a) or (b) may be delivered
electronically and if so delivered, shall be deemed to have been delivered on the date (i) on which RailAmerica posts such documents, or provides a link thereto on the Borrower’s website on the Internet at the website address listed in
Section 13.2; or (ii) on which such documents are posted on RailAmerica’s behalf by Administrative Agent on an Internet or intranet website maintained by Administrative Agent, if any, to which each Lender and the Administrative
Agent have access (whether a commercial, third-party website or whether sponsored by the Administrative Agent) including, to the extent the Lenders and the Administrative Agent have access thereto and such documents are available thereon, the EDGAR
database and sec.gov; provided that RailAmerica shall notify the Administrative Agent of the posting of any such documents. 
 (l) RailAmerica hereby acknowledges that certain of the Lenders (each, a “Public Lender”) may have personnel who do not wish to receive material non-public information with respect to
RailAmerica or its Affiliates, or the respective securities of any of the foregoing, and who may be engaged in investment and other market-related activities with respect to such Persons’ securities. RailAmerica hereby agrees that it will use
commercially reasonable efforts to identify that portion of the Communications that may be distributed to the Public Lenders and that (w) all such Communications shall be clearly and conspicuously marked “PUBLIC” which, at a minimum,
shall mean that the word “PUBLIC” shall appear prominently on the first page thereof; (x) by marking Communications “PUBLIC,” the Borrowers shall be deemed to have authorized the Administrative Agent and the Lenders to treat
such Communications as not containing any material non-public information (although it may be sensitive and proprietary) with respect to the Borrowers or their securities for purposes of United States Federal and state securities laws
(provided, however, that to the extent such Communications constitute Information, they shall be treated as set forth in Section 13.16); (y) all Communications marked “PUBLIC” are permitted to be made
available through a portion of the Platform designated “Public Side Information;” and (z) the Administrative Agent 

  
 -10-

 
shall be entitled to treat any Communications that are not marked “PUBLIC” as being suitable only for posting on a portion of the Platform not designated “Public Side
Information.” 
 (q) Section 9.10 of the Credit Agreement shall be amended by (i) replacing clause
(a) thereof in its entirety with the following: 
 “(a) Each Borrower will cause any direct or indirect Restricted
Domestic Subsidiary formed or otherwise purchased or acquired after the Closing Date (including pursuant to a Permitted Acquisition) that is a Wholly-Owned Subsidiary of RailAmerica and each Wholly-Owned Subsidiary of RailAmerica that becomes or is
designated a Restricted Domestic Subsidiary after the Closing Date and each Excluded Entity (other than the Specified Entity listed on Schedule 1.1(d)) that obtains any assets (other than Equity Interests in another Restricted Subsidiary that would
also qualify as an Excluded Entity) to execute a supplement to each of the Guarantee and the Security Agreements, substantially in the form of Annex B or Annex 1, as applicable, to the respective agreement in order to become a Guarantor under the
Guarantee and a grantor under the Security Agreements and to cause such Subsidiary to take all such actions required under the Security Agreements, to perfect the security interest in the Collateral of such Restricted Domestic Subsidiary. The
Borrowers shall also cause to be delivered to the Collateral Agent (or in the case of Equity Interests that would constitute Fixed Asset Collateral, the Fixed Asset Collateral Agent) for pledging under the applicable Security Agreement (A) the
certificates, if any, evidencing all of the Equity Interests of any Subsidiary (other than an Excluded Entity that has no assets other than Equity Interests of another Subsidiary that would also qualify as an Excluded Entity and other than the
Specified Entity listed on Schedule 1.1(d)) owned by a Credit Party and formed or otherwise purchased or acquired after the Closing Date, together with undated stock powers or other appropriate instruments of transfer executed and delivered in blank
by a duly authorized officer of such Credit Party (provided that not more than 65% of the voting Equity Interests of any Foreign Subsidiary that is a direct Subsidiary of a Domestic Subsidiary shall be required to be so delivered or so
pledged) and (B) all intercompany notes owing from such Subsidiary to any Credit Party, together with instruments of transfer executed and delivered in blank by a duly authorized officer of such Credit Party. Notwithstanding the foregoing, the
Borrowers shall not be required to, nor shall any Borrower be required to cause any Restricted Subsidiary to, grant any security in any assets of any new direct or indirect Restricted Domestic Subsidiary or to require any new direct or indirect
Restricted Domestic Subsidiary to become a Guarantor under the Guarantee and a grantor under the Security Agreements to the extent that such new 

  
 -11-

 
Restricted Domestic Subsidiary shall be restricted from pledging such assets by any valid and enforceable contractual obligation (to the extent such restriction is not overridden by the UCC and
other than any contractual obligation in connection with any Indebtedness incurred or outstanding pursuant to Section 10.1(i) or (m)); provided that (i) the Total Assets of each such new Restricted Subsidiary are less than $25.0
million and the Total Assets of all such Persons that become Restricted Subsidiaries are less than $75.0 million in the aggregate and (ii) such restriction was not incurred in connection with, or in contemplation of, such Person becoming a
Restricted Subsidiary. Notwithstanding the foregoing, in the event that any Subsidiary is or becomes an obligor under any Indebtedness incurred pursuant to Section 10.1(i) or (m), then each Borrower will immediately cause such Subsidiary to
execute a supplement to each of the Guarantee and each Security Agreement, substantially in the form of Annex B or Annex 1, as applicable, to the respective agreement in order to become a Guarantor under the Guarantee and a grantor under each
Security Agreement and to cause such Subsidiary to take all such actions required under each Security Agreement, to perfect the security interest in the Collateral of such Subsidiary.” 
 and (ii) replacing the number “30” in clause (b) thereof with the number “60”. 
 (r) Section 9.12 of the Credit Agreement shall be amended by replacing the second sentence thereof in its entirety with the following: 

“Notwithstanding the foregoing, Mortgages shall not be given if third party consents are required nor will Mortgages be recorded in
states with (a) a significant Mortgage recording tax such as Alabama, Kansas (to the extent they are not recorded under the Secured Notes Indenture or the Term Loan Credit Agreement and are not recorded to secure any other obligations secured
pursuant to Section 10.2(j) or (k)) and Virginia or (b) an unreasonable administrative burden in connection with commercial revolving credit mortgages such as New York (such that they are not recorded under the Secured Notes Indenture or
the Term Loan Credit Agreement and are not recorded to secure any other obligations secured pursuant to Section 10.2(j) or (k)), unless, in either case, the Fixed Charge Coverage Ratio for the last Test Period at the end of which
Section 9.1 Financials were required to have been delivered falls below 1.75, at which point each Credit Party shall cause, within 60 days, such Mortgages to be recorded).” 

  
 -12-

 (s) Section 9.13 of the Credit Agreement shall be amended by replacing the proviso to
the first sentence thereof in its entirety with the following: 
 “provided, however, that, with respect to
After Acquired Property that consists of real property, any such Mortgages shall not be recorded in states with a significant mortgage recording tax such as Alabama, Kansas (to the extent they are not recorded under the Secured Notes Indenture or
the Term Loan Credit Agreement and are not recorded to secure any other obligations secured pursuant to Section 10.2(j) or (k)) and Virginia or (b) an unreasonable administrative burden in connection with commercial revolving credit
mortgages such New York (such that they are not recorded under the Secured Notes Indenture or the Term Loan Credit Agreement and are not recorded to secure any other obligations pursuant to Section 10.2(j) or (k)) unless, in either case, the
Fixed Charge Coverage Ratio for the last Test Period at the end of which Section 9.1 Financials were required to have been delivered falls below 1.75” 
 (t) Section 9.16 of the Credit Agreement shall be replaced in its entirety with the word “[Reserved].” 
 (u) Section 9.17 of the Credit Agreement shall be replaced in its entirety with the following: 
 “9.17 Post-Closing Requirements. Within one hundred twenty days (120) days after the Amendment No. 1 Effective Date, unless waived or extended by the Collateral Agent in its
sole discretion, the Fixed Asset Collateral Agent and the Collateral Agent shall have received each of the following: 
 (i) with
respect to each Mortgage encumbering Mortgaged Property, an amendment thereof (each a “Mortgage Amendment”), duly executed and acknowledged by the applicable Credit Party, the Fixed Asset Collateral Agent, and in form for recording
in the recording office where each Mortgage was recorded, together with such certificates, affidavits, questionnaires or returns as shall be required in connection with the recording or filing thereof under applicable law, in each case in form and
substance reasonably satisfactory to the Collateral Agent and the Fixed Asset Collateral Agent; 
 (ii) opinions of counsel for
the Borrowers and the applicable Credit Parties in form and substance reasonably satisfactory to the Fixed Asset Collateral Agent and the Collateral Agent; and 
 (iii) evidence acceptable to the Collateral Agent of payment by the Credit Parties of all applicable mortgage recording taxes, fees, charges, costs and expenses required for the recording of the Mortgage
Amendments.” 
 (v) Section 9.18 of the Credit Agreement shall be deleted in its entirety. 

  
 -13-

 (w) Section 10.1 of the Credit Agreement shall be amended by (i) replacing clause
(g) thereof in its entirety with the following 
 “(g) Indebtedness in respect of (A) Hedge Agreements entered
into in the ordinary course of business (and not for speculative purposes) in order to protect RailAmerica or any of the Restricted Subsidiaries against fluctuations in interest rates, currency exchange rates or commodity prices; (B) Cash
Management Agreements; and (C) any Hedge Agreements otherwise permitted hereunder between RailAmerica and a Restricted Subsidiary, on the one hand, and any Person that is a lender under the Term Loan Credit Agreement or an Affiliate of a lender
under the Term Loan Credit Agreement at the time such Hedge Agreement is entered into;” 
 (ii) replacing clause (i) thereof in its
entirety with the following: 
 “(i) (A)(I) Indebtedness of the Credit Parties under the Secured Notes in an aggregate
principal amount not exceeding the aggregate principal amount of Secured Notes outstanding immediately following the consummation of the Tender Offer and (II) one or more successive issuances or incurrences of Permitted Refinancing Indebtedness in
respect of the Indebtedness referred to in clause (A)(I) of this Section 10.1(i) and (B)(I) Indebtedness under the Term Loan Credit Agreement in an aggregate principal amount not to exceed (x) $585,000,000 plus (y) to the extent
permitted under Section 2.15 of the Term Loan Credit Agreement as in effect on the Amendment No. 1 Effective Date, $150,000,000 and (II) one or more successive issuances or incurrences of Permitted Refinancing Indebtedness in respect of
the Indebtedness referred to in clause (B)(I) of this Section 10.1(i);” 
 (iii) adding the words “or any proceeds used to
effectuate a Specified Equity Contribution” at the end of the parenthetical in subclause (y) of clause (k) thereof, 
 and
(iv) replacing clause (c) of clause (m) thereof in its entirety with the following: “the terms of such Indebtedness do not provide for any mandatory redemption or prepayment or mandatory offer to purchase or prepay on or prior to
the Maturity Date (other than (i) customary offers to purchase upon a change of control, asset sale or event of loss, (ii) other prepayment or redemption events not more onerous to RailAmerica and its Restricted Subsidiaries than those set
forth in Section 5.2 of the Term Loan Credit Agreement as in effect on the Amendment No. 1 Effective Date and (iii) customary acceleration rights after an event of default),”. 

(x) Section 10.2 of the Credit Agreement shall be amended by: 

(i) in clause (h) thereof, replacing the words “are junior to the Liens securing the Obligations” with “have Junior
Lien Priority (and are subject to the Intercreditor Agreement in such capacity)”; 

  
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 (ii) in clause (j) thereof, (A) replacing the words “are junior to the Liens
securing the Obligations, Liens on Fixed Asset Collateral” with the words “have Junior Lien Priority (and are subject to the Intercreditor Agreement in such capacity), Liens on Fixed Asset Collateral securing Indebtedness permitted to be
incurred pursuant to Section 10.1”, (B) deleting “(x)” and (C) deleting clause (y) of the proviso thereto; 
 (iii) in clause (k) thereof, (A) replacing the words “are junior to the Liens securing the Obligations” with the words “have Junior Lien Priority (and are subject to the
Intercreditor Agreement in such capacity)” and (B) deleting the words “the Consolidated First Lien Secured Debt to Consolidated EBITDA Ratio or”; and 
 (iv) adding a new clause (l) thereof which shall state as follows: 

“(l) Liens on Fixed Asset Collateral pursuant to the Term Loan Security Documents and subject to the Intercreditor Agreement in the
capacity of “Term Loan Obligations” securing Indebtedness permitted to be incurred pursuant to clause (C) of Section 10.1(g).” 
 (v) adding the following sentence at the end of Section 10.2, “Notwithstanding anything to the contrary contained in herein, in no event shall RailAmerica or any of its Restricted Subsidiaries
allow or suffer to exist that the Applicable Authorized Representative (as defined in the Intercreditor Agreement), in its capacity as such, shall be a representative of any Indebtedness that is secured with a Lien that has Junior Lien Priority.

 (y) Section 10.3(f) of the Credit Agreement shall be amended by replacing the word “that” with the word
“than”. 
 (z) Section 10.4 of the Credit Agreement shall be amended by replacing clause (ii) thereof with
the following: “(ii) sell to any Person any Equity Interests owned by it of any Restricted Subsidiary, except that:” and replacing clause (b) thereof in its entirety as follows: 

“RailAmerica and the Restricted Subsidiaries may sell, transfer or otherwise dispose of other assets (other than Accounts) for at
least Fair Market Value of the assets sold or otherwise disposed of; provided that (i) the consideration received for any such sales, transfers and disposals shall consist of not less than 75% cash consideration or Permitted Investments;
provided that for the purposes of this clause (i) the following shall be deemed to be cash: (A) any liabilities (as shown on RailAmerica’s or such Restricted Subsidiary’s most recent balance sheet provided hereunder or in
the footnotes thereto) of RailAmerica or such Restricted Subsidiary assumed by the transferee with respect to the applicable sale, transfer 

  
 -15-

 
or disposal, as to which RailAmerica and all of the Restricted Subsidiaries shall have been released by all applicable creditors in writing, other than liabilities that are by their terms
(1) subordinated to the payment in cash of the Obligations or (2) in the case of a sale by a Borrower or a Subsidiary Guarantor, not secured by the assets that are the subject of such sale, transfer or disposal, (B) any securities
received by the Person making such sale, transfer or disposal from the transferee that are converted by such Person into cash (to the extent of the cash received) within 180 days following the closing of the applicable sale, transfer or disposal and
(C) any Designated Non-Cash Consideration received by RailAmerica or any Restricted Subsidiary in such Asset Sale having an aggregate Fair Market Value, taken together with all other Designated Non-Cash Consideration received pursuant to this
clause (C) that is at that time outstanding, not to exceed the greater of (x) $45.0 million and (y) 3.0% of Total Assets at the time of the receipt of such Designated Non-Cash Consideration, with the Fair Market Value of each
item of Designated Non-Cash Consideration being measured at the time received and without giving effect to subsequent changes in value; and (ii) after giving effect to any such sale, transfer or disposition, no Default or Event of Default shall
have occurred and be continuing. Unless a permanent prepayment of Term Loan Facility Indebtedness or Indebtedness comprising Other Pari Passu Lien Obligations is made within 365 days of the date of receipt of such Net Proceeds, the Net Proceeds
thereof shall be used within 365 days of the date such Net Proceeds are received by RailAmerica or a Restricted Subsidiary to make an Investment in (a) any one or more businesses (provided that such Investment in any business is in the
form of the acquisition of Equity Interests and results in RailAmerica or a Restricted Subsidiary, as the case may be, owning an amount of the Equity Interests of such business such that it constitutes a Restricted Subsidiary), (b) capital
expenditures for RailAmerica and its Restricted Subsidiaries or (c) acquisitions of other assets that, in each of (a), (b) and (c), are used or useful in a Similar Business that becomes a Restricted Subsidiary or is held by RailAmerica or
a Restricted Subsidiary; provided further that, in the case of each of (a), (b) and (c), to the extent the disposition giving rise to such Net Proceeds was of Fixed Asset Collateral, such Investment is concurrently added to the
Fixed Asset Collateral; provided further that if required by the terms of any Indebtedness incurred or outstanding under Section 10.1(h), (i), (k) or (m) to place such Net Proceeds in a collateral or control account with
or on behalf of a representative of such Indebtedness, the Net Proceeds from any such Asset Sale pursuant to this Section 10.4(b) of Fixed Asset Collateral shall be paid directly by the purchaser thereof to the Fixed Asset Collateral Agent to
be held in trust in an Asset Sale Proceeds Account for application in accordance with the terms of this Agreement; provided further that RailAmerica shall immediately after or prior to opening or designating any account or an Asset
Sale Proceeds Account send a written notice identifying such account to the Administrative Agent and the Fixed Asset Collateral Agent; provided further that (i) RailAmerica shall immediately after to or prior to opening or
designating any account as an Asset Sale Proceeds 

  
 -16-

 
Account send a written notice identifying such account to the Administrative Agent and he Collateral Agent, (ii) the Asset Sale Proceeds Account shall not be subject to any Liens, other than
the Lien of the Fixed Asset Collateral Agent, (iii) neither RailAmerica nor any Restricted Subsidiary shall commingle the amounts in the Asset Sale Proceeds Account with any other amounts, other than any other proceeds of an Asset Sale or other
sale of Fixed Asset Collateral and (iv) the proceeds of any Asset Sale permitted by Section 10.4 (other than this Section 10.4(b)) shall not be required to be deposited in the Asset Sale Proceeds Account;” 

(aa) Section 10.6(b) of the Credit Agreement shall be amended and restated in its entirety as follows: 

“(A) any Restricted Payment in exchange for, or out of the proceeds of the substantially concurrent sale (other than to a Restricted
Subsidiary) of, Equity Interests of RailAmerica (other than any Disqualified Capital Stock or pursuant to a Specified Equity Contribution) (“Refunding Capital Stock”) and (B) if immediately prior to the redemption, repurchase,
retirement or other acquisition of any Equity Interests of RailAmerica (“Retired Capital Stock”) the Fixed Charge Coverage Ratio for the last Test Period at the end of which Section 9.1 Financials were required to have been
delivered would have been at least 2.00 to 1.00, the declaration and payment of dividends on the Refunding Capital Stock (other than Refunding Capital Stock the proceeds of which were used to redeem, repurchase, retire or otherwise acquire any
Equity Interests of RailAmerica) in an aggregate amount per year no greater than the aggregate amount of dividends per annum that was declarable and payable on such Retired Capital Stock immediately prior to such retirement;” 

(bb) Section 10.6(c) of the Credit Agreement shall be amended by adding the words “to the extent not used to effectuate a
Specified Equity Contribution,” at the beginning of subclause (i) thereof; 
 (cc) Section 10.6(g) of the Credit
Agreement shall be amended and restated in its entirety as follows: 
 “the payment of dividends on RailAmerica’s
Common Stock after the Issue Date, of up to 6% per annum of the net cash proceeds received by RailAmerica in any public offering of its Common Stock following June 23, 2009 (other than (w) public offerings registered on Form S-8,
(x) any public sale constituting an Excluded Contribution, (y) any net cash proceeds used to incur Indebtedness pursuant to Section 10.1(k) and (z) any such net cash proceeds raised in order to effectuate a Specified Equity
Contribution)”; 
 (dd) Section 10.6(k) of the Credit Agreement shall be amended by replacing the reference to
“the Company” therein to “RailAmerica”. 

  
 -17-

 (ee) Section 10.7 of the Credit Agreement shall be amended and restated in its entirety
as follows: 
 “(a) RailAmerica will not, and will not permit any of the Restricted Subsidiaries to, make directly or
indirectly, any payment or other distribution (whether in cash, securities or other property) of (or in respect of) any principal of any Junior Financing, or any payment or other distribution (whether in cash, securities or other property),
including any sinking fund or similar deposit, on account of the purchase, redemption, retirement, acquisition, cancellation or termination of any Junior Financing; except (A) to the extent such payments are made using the Available
Amount Basket, (B) so long as both immediately before and immediately after giving effect to such payment (i) no Default or Event of Default shall have occurred and be continuing and (ii) the Consolidated Total Debt to Consolidated
EBITDA Ratio would be less than 4.0 to 1.0; provided that this clause (B) shall not allow payments of any Indebtedness that is subordinated in right of payment to any of the Obligations, (C) to the extent such payment is made with
Qualified Capital Stock of RailAmerica or (D) with Permitted Refinancing Indebtedness in respect of such Indebtedness. 

(b) RailAmerica will not, and will not permit any Restricted Subsidiary, to amend, modify or waive any of its rights under any agreement
governing or relating to any Junior Financing to the extent any such amendment, modification or waiver would be materially adverse to the Lenders. RailAmerica will not amend the terms of any Junior Financing in a manner that would accelerate the
date on which RailAmerica is required to make any payment of principal or interest or any other amount thereon. 
 (ff)
Section 10.9 of the Credit Agreement shall be amended by (i) replacing the words “Consolidated Senior Secured Debt to Consolidated EBITDA Ratio” with the words “Consolidated Senior Secured Net Debt to Consolidated EBITDA
Ratio” in each place they appear in such Section, (ii) replacing the grid therein in its entirety with the following: 
  

									
	 Year
	  	First Quarter	  	Second Quarter	  	Third Quarter	  	Fourth Quarter
	 2011
	  	N/A	  	N/A	  	5.00:1.00	  	5.00:1.00
	 2012
	  	5.00:1.00	  	5.00:1.00	  	5.00:1.00	  	4.50:1.00
	 2013
	  	4.50:1.00	  	4.25:1.00	  	4.25:1.00	  	4.00:1.00
	 2014
	  	4.00:1.00	  	4.00:1.00	  	4.00:1.00	  	3.75:1.00
	 2015
	  	3.75:1.00	  	3.75:1.00	  	3.75:1.00	  	3.50:1.00
	 Thereafter
	  	3.25:1.00	  	3.25:1.00	  	3.25:1.00	  	3.25:1.00

  
 -18-

 and (iii) adding the following after the grid: 

“For purposes of determining compliance with this Section 10.9, the net cash proceeds from the issuance and sale
of Equity Interests of RailAmerica (other than Disqualified Capital Stock) received by RailAmerica after the end of the relevant Test Period and on or prior to the date that is ten days after the day on which Section 9.1 Financials are required
to be delivered (without giving effect to any grace period) for the last fiscal quarter in such Test Period will, at the request of RailAmerica, be included in the calculation of Consolidated EBITDA solely for the purposes of determining compliance
with this Section 10.9 at the end of such Test Period and applicable subsequent Test Periods which include such fiscal quarter but not for determining pro forma compliance with this Section 10.9 to determine the permissibility of a
transaction (such net cash proceeds so received by RailAmerica and so included in the calculation of Consolidated EBITDA, a “Specified Equity Contribution”), subject to the following terms and conditions: (a) in each four
fiscal quarter period, there shall be at least two fiscal quarters in respect of which no Specified Equity Contribution is made, (b) the amount of any Specified Equity Contribution shall be no greater than the amount required to cause the
Borrowers to be in compliance on a Pro Forma Basis with this Section 10.9, (c) all Specified Equity Contributions shall be disregarded for making any other determination herein or any other Credit Document, (d) no more than four
Specified Equity Contributions shall be made prior to the Maturity Date, (e) there shall be no reduction in Indebtedness in connection with any Specified Equity Contributions for determining compliance with this Section 10.9 and no
Specified Equity Contribution shall be included as cash for purposes of calculating clause (y) of the definition of Consolidated Senior Secured Net Debt and (f) the proceeds of the Specified Equity Contribution shall immediately be used to
prepay Loans to the extent required by Section 5.2.” 
 (gg) Section 10.11(a) of the Credit Agreement shall be
amended by replacing the words “and the Secured Note Indenture” with the words “, the Term Loan Credit Agreement and the Secured Notes Indenture”. 
 (hh) Section 10.12 of the Credit Agreement shall be amended by adding the following as the last sentence of such section: “The Specified Entities listed on Schedule 1.1(d) shall only be used to
conduct business relating to the making of contributions for candidates and other political purposes.” 
 (ii) A new
Section 10.14 shall be added to Section 10 of the Credit Agreement, which will state: “10.14 Amendment No. 1 Effective Date Repayment. RailAmerica shall not fail to repay, on the Amendment No. 1 Effective Date,
Loans outstanding on such date to the extent the proceeds of Term Loan Facility Indebtedness exceeds the amount 

  
 -19-

 
necessary to finance the tender consideration (including tender premiums and interest) in connection with the Tender Offer and pay fees and expenses in connection with the entry into the Term
Loan Facility, the making of the Tender Offer and this Amendment No. 1.” 
 (jj) Section 11.3 of the Credit
Agreement shall be amended by deleting the words “Section 9.16,”. 
 (kk) Section 11.4 of the Credit Agreement
shall be amended by (i) adding the words “(the “Threshold Debt”) after the word “Subsidiaries” in clause (a)(i) and (ii) replacing the word “Indebtedness” with the words “Threshold Debt”
each time it appears in clause (a)(ii) and (b). 
 (ll) Section 12.6(a) of the Credit Agreement shall be amended by
(A) adding the words “(except that in the case of any Collateral held by the Collateral Agent on behalf of the Lenders or the Letter of Credit Issuer under any of the Credit Documents, the retiring Collateral Agent shall continue to hold
such Collateral as nominee until such time as a successor Collateral Agent is appointed)” at the end of clause (i) in the fifth sentence thereof and (B) adding the following parenthetical at the end of such Section 12.6(a):
“(or in the capacity set forth in the parenthetical in clause (i) above)”. 
 (mm) Section 12.10 of the
Credit Agreement shall be amended (i) by adding the words “(and make amendments and modifications to the Intercreditor Agreement contemplated by the Intercreditor Agreement)” after the words “Intercreditor Agreement” in
subclause (a) thereof and (ii) to add the following sentence at the end of such Section: 
 “It is hereby agreed
that, for the purposes of Section 6.5 of the Fixed Asset Security Agreement and Section 5.01 of each Mortgage, the security interests granted thereunder shall not terminate until all Obligations (other than obligations under Secured Hedge
Agreements and Secured Cash Management Agreements not yet due and payable) shall have been paid in full in cash. Furthermore, the Lenders authorize and instruct the Administrative Agent to appoint the Term Loan Agent, one of its Affiliates or
another Person appointed by the Term Loan Agent, to become the “Collateral Agent” under the Intercreditor Agreement in accordance with the terms thereof on or after the time that no Secured Notes are outstanding (and to take all actions
and to execute and deliver any and all documents the Administrative Agent determines are necessary or advisable to so execute and deliver in accordance therewith, and the Borrowers agree to pay the expenses of the Administrative Agent in connection
with the foregoing).” 
 (nn) A new Section 12.12 shall be added to Section 12 of the Credit Agreement, which
will state: 
 “12.12 Collateral Release. In addition to any provisions of the Security Documents, each of the
Secured Parties irrevocably authorize each of the Collateral Agent and the Fixed Asset Collateral Agent , at its option and in its discretion, 

  
 -20-

	 	(a)	to release any Lien on any property granted to or held by the Collateral Agent under any Credit Document (i) upon the Final Date, (ii) that is sold or to be
sold as part of or in connection with any sale permitted hereunder or under any other Loan Document to a Person that is not a Credit Party or (iii) that constitutes “Excluded Property” (as such term is defined in each of the Security
Agreements) or locomotives or railcars subject to a lease with any lessor that is not a Credit Party; 

  

	 	(b)	to release any Subsidiary Guarantor from its obligations under this Agreement and other Security Documents if such Person ceases to be a Subsidiary as a result of a
transaction permitted hereunder; and 

  

	 	(c)	to subordinate or release any Lien on any property granted to or held by the Collateral Agent under any Credit Document to the holder of any Lien on such property that
is granted pursuant to Section 10.2(c)(A), (f) or (g). 

 Upon request by the Collateral Agent at any
time, the Borrowers will provide an officer’s certificate confirming the permissibility under the Credit Documents of any transaction in connection with which the any Credit Party is seeking a release of Collateral under this
Section 12.12.” 
 (oo) Section 13.1 of the Credit Agreement shall be amended by adding the following sentence at
the end of such Section 13.1(a): “Notwithstanding the foregoing, RailAmerica will not enter into any amendment contemplated by the second sentence of Section 11 of the Intercreditor Agreement without the prior written consent of the
Administrative Agent (but it being understood that only the consent of the Administrative Agent (and no Lender or Secured Party in its capacity as such) shall be required to effectuate any such amendment pursuant to such second sentence).”

 (pp) Section 13.5 of the Credit Agreement shall be amended by adding the words “whether brought by any Credit
Party, any stockholder or creditor of any Credit Party, or any other Person,” immediately prior to the words “including reasonable and documented”. 
 (qq) Section 13.6 of the Credit Agreement shall be amended by (A) adding the words “if the Administrative Agent has been informed thereof,” immediately before the words “the
Administrative Agent shall provide a second notice to RailAmerica” in clause (a)(i)(A) thereof and (B) replacing the word “Subsidiaries” with the word “Affiliates” in the proviso to clause (b) thereof. 

Section 2. Other Amendments. Effective as of the Effective Date: 

(a) The Intercreditor Agreement is hereby amended and restated in its entirety to be in the form of Exhibit C hereto. 

  
 -21-

 (b) Exhibit K to the Credit Agreement is hereby deleted in its entirety. 

(c) Exhibit N attached hereto shall be deemed to be Exhibit N of the Credit Agreement. 

(d) Schedules 1.1(c) and 1.1(d) attached hereto are deemed to be Schedules 1.1(c) and 1.1(d) to the Credit Agreement. 

Section 3. Effectiveness. This Amendment will become effective as of the date each of the following conditions
precedent shall have been (or are or will be substantially concurrently therewith) satisfied or waived by the Administrative Agent (the “Amendment No. 1 Effective Date”): 

(a) the Administrative Agent shall have received executed signature pages hereto from the Required Lenders under and as defined in the
Credit Agreement, the Borrowers and each of the other parties listed on the signature pages hereto by no later than March 1, 2012; 
 (b) the Administrative Agent shall have received a certificate of the secretary or assistant secretary of each Credit Party dated the Amendment No. 1 Effective Date, certifying (A) that attached
thereto is a true and complete copy of each Organizational Document of such Credit Party certified (to the extent applicable) as of a recent date by the Secretary of State of the state of its organization, (B) that attached thereto is a true
and complete copy of resolutions duly adopted by the Board of Directors of such Credit Party authorizing the execution, delivery and performance of this Amendment (and all documents to be entered into in connection herewith) to which such Person is
a party and that such resolutions have not been modified, rescinded or amended and are in full force and effect and (C) as to the incumbency and specimen signature of each officer executing this Amendment (and all documents to be entered into
in connection herewith) or any other document delivered in connection herewith on behalf of such Credit Party (together with a certificate of another officer as to the incumbency and specimen signature of the secretary or assistant secretary
executing the certificate in this clause (b)); 
 (c) a certificate as to the good standing of each Credit Party (in
so-called “long-form” if available) as of a recent date, from such Secretary of State (or other applicable Governmental Authority), as well as such other documents as the Administrative Agent may reasonably request; 

(d) the Administrative Agent shall have received a solvency certificate (in substantially the same form as the solvency certificate dated
as of the Closing Date) signed by the chief financial officer of RailAmerica; 
 (e) the Administrative Agent shall have
received the results of a recent lien search report in such jurisdictions as may be reasonably requested by the Administrative Agent and such reports shall reflect no Liens other than Liens permitted by Section 10.2 of the Credit Agreement;

  
 -22-

 (f) the Administrative Agent shall have received Joinder Agreements substantially in the
form attached as Exhibit B hereto executed and delivered by the Borrowers, the New Lenders and the Administrative Agent, providing for an increase in Commitments such that, immediately after giving effect to this Amendment and such Joinder
Agreements, the aggregate amount of the Commitments under the Credit Agreement is $100,000,000; 
 (g) the Administrative Agent
shall have received a certificate of the chief executive officer and the chief financial officer of RailAmerica to the effect that the representations and warranties specified in Section 4 of this Amendment are true and correct and no Default
or Event of Default has occurred and is continuing and that each other condition precedent in this Section 2 shall have been satisfied; 
 (h) the Borrowers shall have (i) paid the Administrative Agent or its Affiliates all the fees due to the Administrative Agent or its Affiliates and (ii) reimbursed or paid all expenses required
to be paid or reimbursed by the Borrowers pursuant to the Credit Agreement and Section 9 hereto; 
 (i) the Administrative
Agent shall have received such executed legal opinions of (a) Skadden, Arps, Slate, Meagher & Flom LLP, special New York counsel to the Borrowers (b) Scott Williams, General Counsel to the Borrowers (c) the opinions of
special local counsel to the Borrowers from the jurisdictions listed on Schedule 6.3 to the Credit Agreement, in each case in form and substance reasonably satisfactory to the Administrative Agent; 

(j) (A) the Tender Offer shall not have been amended since February 1, 2012 except as consented to by the Administrative Agent,
(B) an aggregate principal amount of Secured Notes satisfactory to the Administrative Agent shall have been irrevocably accepted for purchase in the Tender Offer by RailAmerica (the “Accepted Notes”) and (C) all conditions
to the consummation of the Tender Offer (other than the actual payment for the Accepted Notes and the effectiveness of this Amendment) shall have been satisfied; 
 (k) the Term Loan Credit Agreement (and all documents related thereto) shall have been fully executed and delivered by all parties thereto, and all conditions precedent to the borrowing thereunder (other
than the actual payment for the Accepted Notes and the effectiveness of this Amendment) shall have been satisfied; 
 (l) the
Intercreditor Agreement substantially in the form of Exhibit C hereto shall have been executed by all parties thereto and be in form and substance reasonably acceptable to the Administrative Agent; 

(m) the Lenders and the Administrative Agent shall have timely received all “know your customer” information that they shall
have requested; and 

  
 -23-

 (n) each Credit Party and the Administrative Agent and/or Collateral Agent shall have
entered into one or more reaffirmation agreements (as to this Agreement and the Security Agreements), in form and substance reasonably satisfactory to the Administrative Agent. 

Section 4. Representations and Warranties of the Borrowers. The Borrowers hereby represent and warrant as of the date
hereof and as of the Amendment Effective Date that: 
 (a) each Credit Party has the corporate or other organizational power and
authority to execute, deliver and carry out the terms and provisions of this Amendment and each other Credit Document executed or to be executed in connection with this Amendment to which it is a party and has taken all necessary corporate or other
organizational action to authorize the execution, delivery and performance of this Amendment and each other Credit Document executed or to be executed in connection with this Amendment to which it is a party. Each Credit Party has duly executed and
delivered this Amendment and each other Credit Document executed or to be executed in connection with this Amendment to which it is a party and this Amendment and each Credit Document executed or to be executed in connection with this Amendment
constitutes the legal, valid and binding obligation of such Credit Party enforceable in accordance with its terms, except as the enforceability thereof may be limited by bankruptcy, insolvency or similar laws affecting creditors’ rights
generally and subject to general principles of equity. 
 (b) neither the execution, delivery or performance by any Credit Party
of this Amendment and each other Credit Document executed or to be executed in connection with this Amendment to which it is a party nor compliance with the terms and provisions thereof nor the consummation of the transactions contemplated hereby or
thereby (including, without limitation, the consummation of the Tender Offer and the incurrence of the Term Loan Facility Indebtedness) will (i) contravene any applicable provision of any material law, statute, rule, regulation, order, writ,
injunction or decree of any court or governmental instrumentality; (ii) result in any breach of any of the terms, covenants, conditions or provisions of, or constitute a default under, or result in the creation or imposition of (or the
obligation to create or impose) any Lien upon any of the property or assets of RailAmerica or any of the Restricted Subsidiaries (other than Liens created under the Credit Documents or securing Term Loan Facility Indebtedness), pursuant to the terms
of any material indenture (including the Secured Note Indenture, any loan agreement, lease agreement, mortgage, deed of trust, agreement or other material instrument to which RailAmerica or any of the Restricted Subsidiaries is a party or by which
it or any of its property or assets is bound); or (c) violate any provision of the certificate of incorporation, By-Laws or other constitutional documents of RailAmerica or any of the Restricted Subsidiaries; 

(c) each of the representations and warranties of any Credit Party contained in the Credit Agreement or any other Credit Document are
true and correct in all material respects (unless stated to relate to a specific earlier date, in which case, such representations and warranties are true and correct in all material respects as of such earlier date); and 

  
 -24-

 (d) no Default or Event of Default has occurred and is continuing. 

Section 5. Counterparts. This Amendment may be executed in any number of counterparts and by different parties hereto
on separate counterparts, each of which when so executed and delivered shall be deemed to be an original, but all of which when taken together shall constitute a single instrument. Delivery of an executed counterpart of a signature page of this
Amendment by facsimile transmission shall be effective as delivery of a manually executed counterpart hereof. 
 SECTION 6.
Applicable Law. THIS AMENDMENT AND THE RIGHTS AND OBLIGATIONS OF THE PARTIES HEREUNDER SHALL BE GOVERNED BY, AND CONSTRUED AND INTERPRETED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK. 

Section 7. Headings. The headings of this Amendment are for purposes of reference only and shall not limit or
otherwise affect the meaning hereof. 
 Section 8. Effect of Amendment. Except as expressly set forth herein,
this Amendment shall not by implication or otherwise limit, impair, constitute a waiver of or otherwise affect the rights and remedies of the Lenders or the Administrative Agent under the Credit Agreement or any other Credit Document, and shall not
alter, modify, amend or in any way affect any of the terms, conditions, obligations, covenants or agreements contained in the Credit Agreement or any other provision of the Credit Agreement or any other Credit Document, all of which are ratified and
affirmed in all respects and shall continue in full force and effect. 
 Section 9. Costs and Expenses.
Without duplication of any amounts previously paid or reimbursed, the Borrowers hereby agree to pay all reasonable costs and expenses of the Administrative Agent associated with the preparation, execution and delivery of this Amendment, including,
without limitation, the fees and expenses of Cahill Gordon & Reindel LLP, counsel to the Administrative Agent and other out of pocket expenses related hereto. 

[Remainder of Page Intentionally Blank] 

  
 -25-

 IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly executed by
their respective authorized officers as of the day and year first above written. 
  

					
	RAILAMERICA, INC.,
	 as a Borrower

		
	By:	 	 /s/ Randy Pianin

		 	Name:	 	Randy Pianin
		 	Title:	 	Vice President & Treasurer
	
	RAILAMERICA TRANSPORTATION CORP.,
	 as a Borrower

		
	By:	 	 /s/ Scott Williams

		 	Name:	 	Scott Williams
		 	Title:	 	President

  

 
					
	CITIBANK, N.A.,
	 as Administrative Agent, Swingline Lender, Letter of Credit Issuer and Lender

		
	By:	 	 /s/ Caesar Wyszomirski

		 	Name:	 	Caesar Wyszomirski
		 	Title:	 	Vice President

  

 
					
	Morgan Stanley Bank, N.A.,
	 as a Lender

		
	By:	 	 /s/ Scott Taylor

		 	Name:	 	Scott Taylor
		 	Title:	 	Authorized Signatory
	
	 BMO Harris Bank, N.A.,
 as a Lender

		
	By:	 	 /s/ William Thompson

		 	Name:	 	William Thompson
		 	Title:	 	Senior Vice President

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