Exhibit 10.1

SECOND AMENDMENT TO AGREEMENT

This SECOND AMENDMENT TO AGREEMENT (this “Agreement”) is entered into as of
October 14, 2011, by and between Great Lakes Aviation, Ltd., an Iowa
corporation, with its principal place of business at 1022 Airport Parkway,
Cheyenne, Wyoming 82001 (“Great Lakes”) and Raytheon Aircraft Credit
Corporation, a Kansas corporation, with its principal place of business at 8300
E. Thorn Drive, Suite 100, Wichita, Kansas 67226 (“RACC”).

WHEREAS, Great Lakes and RACC are parties to twenty-five (25) separate Amended
and Restated Promissory Notes or Second Amended and Restated Promissory Notes,
each of which is dated March 23, 2007, and as amended on June 10, 2011 and
August 31, 2011 (each a “Promissory Note” and collectively, the “Promissory
Notes”) and twenty-five (25) separate Security Agreements or Amended and
Restated Security Agreements, each of which is dated as of December 31, 2002, as
each of which was amended by a First Amendment dated as of March 23, 2007, the
supplement to which is dated May 1, 2008, and each of which was amended by a
Second Amendment dated June 10, 2011, and each of which was further amended by a
Third Amendment dated August 31, 2011 (each originally executed and as amended,
restated or supplemented and currently in effect, a “Security Agreement” and
collectively, the “Security Agreements”), and pursuant to which RACC is
currently financing Great Lakes’ purchase of twenty-five (25) used Beech 1900D
Airliners that have the following manufacturer’s serial numbers: UE-100, UE-122,
UE-153, LIE-154, UE-169, UE-170, UE-184, UE-192, UE-195, UE-201, UE-202, UE-208,
UE-210, UE-211, UE-219, UE-220, UE-240, UE-245, UE-247, UE-251, UE-253, UE-254,
UE-255, UE-257 and UE-261 (the Promissory Notes and Security Agreements are
hereinafter sometimes referred to collectively, but as further modified in the
next recital, as the “Finance Documents”);

WHEREAS, by an Agreement dated as of June 10, 2011, as amended by an Amendment
to Agreement dated as of August 31, 2011 (collectively, as so amended and
together with the amendments and other documents executed in connection with
such Agreement and such Amendment, the “Original Agreement”) Great Lakes and
RACC agreed, in some specific respects, to modify certain of the “Finance
Documents” (which term, as used hereinafter, shall mean the Finance Documents as
amended and modified by, or in connection with, the Original Agreement);

WHEREAS, the Promissory Notes, as modified by the Original Agreement, require
Great Lakes to pay in full the entire remaining balance of principal and
interest due under each Promissory Note (the “Balloon Payments”) on or before
October 17, 2011 (the “Amended Balloon Payment Date”) and, as of the date of
this Agreement, Great Lakes has disclosed and acknowledges that it is unable to
timely and fully pay the Balloon Payments to RACC as required under the
Promissory Notes;

WHEREAS, Great Lakes has requested that RACC agree to extend the Amended Balloon
Payment Date from October 17, 2011 to November 17, 2011; and

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WHEREAS, on and subject to the terms and conditions provided in this Agreement,
RACC is willing to agree to so extend the Amended Balloon Payment Date,

NOW, THEREFORE, in consideration of the foregoing premises, and for other good
and valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, and fully intending to be legally bound by this Agreement, the
parties hereto agree as follows:

1. Extension of Balloon Payment Date; Extension Fee.

(a) On the terms and conditions provided in this Agreement, the parties hereto
hereby agree that Amended Balloon Payment Date is extended from October 17, 2011
to November 17, 2011. Great Lakes irrevocably and unconditionally agrees (i) to
make payments of $27,600 on each Promissory Note on or before October 30, 2011,
and (ii) to pay any and all amounts outstanding and unpaid, including, without
limitation, all principal and accrued interest, on each Promissory Note on or
before November 17, 2011. The modification to each of the Promissory Notes
agreed to under this Agreement shall be reflected in a Third Amendment to
Amended and Restated Promissory Note or a Third Amendment to Second Amended and
Restated Promissory Note (as the case may be) to each Promissory Note dated the
date hereof and shall be in the form attached to this Agreement as Exhibit A.
For the avoidance of any possible doubt, the payment and performance by Great
Lakes of each and all of its obligations under and in connection with, among
other things, the Promissory Notes, as amended by the Third Amendment to Amended
and Restated Promissory Note or Third Amendment to Second Amended and Restated
Promissory Note (as the case may be) provided for under this Agreement, are, and
continue to be, secured by each Security Agreement, and each Promissory Note, as
so amended, is and constitutes a “Transaction Document”, as that term is defined
in the Amended and Restated Restructuring Agreement dated as of March 9, 2007 by
and between Great Lakes and RACC. To memorialize that understanding, the parties
hereto on the date hereof are entering into a Fourth Amendment to the Security
Agreements, which shall be in the form attached to this Agreement as Exhibit B.

(b) Great Lakes agrees to pay to RACC, on the date hereof, an extension fee in
the amount of One Hundred Twenty-Five Thousand Dollars ($125,000), which shall
be fully earned when paid and not refundable, and which is in addition to paying
RACC’s reasonable costs and expenses as hereinafter provided.

2. Continued Effectiveness of Finance Documents; No Waiver; Etc.

(a) Except as expressly modified by this Agreement, the parties hereby confirm
and ratify each of the other terms and conditions of the Finance Documents, and
agree that all of the provisions of each Finance Document remain in full force
and effect and Great Lakes hereby confirms and ratifies each of its obligations
under the Finance Documents. The parties also agree that, in addition to any
other Event of Default (as defined in the relevant document), any breach of any
provision of this Agreement shall constitute an immediate Event of Default under
each of the Finance Documents, the Leases (as hereinafter defined) and the
Senior Note Documents (as hereinafter defined, and, collectively with the
Finance Documents and the Leases, the “GLUX/RACC Documents”).

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(b) Great Lakes hereby acknowledges and agrees that except as expressly provided
herein, the GLUX/RACC Documents remain in full force and effect and that, if it
defaults in any of its obligations to RACC, RACC is fully entitled to exercise
any or all of its rights and remedies as provided in, and in accordance with the
provisions of, the GLUX/RACC Documents.

(c) Great Lakes hereby acknowledges and agrees that RACC’s agreement to extend
the Balloon Payment Date in this Agreement does not constitute a waiver or
forgiveness of any obligation and that, in granting the extension under the
Original Agreement and the extension provided herein, RACC is not agreeing to,
or suggesting in any way, that there will or might be any further extension,
accommodation or any waiver of any right or remedy in any of the GLUX/RACC
Documents and Great Lakes acknowledges and agrees that it will not assume or
rely upon the possibility or prospect of any possible future extension or
accommodation by RACC.

3. No Impact on Other Agreements. The parties hereto hereby agree as follows:

(a) Leases. Great Lakes currently is leasing three (3) used Beech 1900D
Airliners under three (3) separate Operating Leases (the “Leases”), each of
which is identified on Exhibit C, which is attached to this Agreement. As
contemplated by the Leases, on or about May 4, 2011 RACC gave Great Lakes a
Notice of Termination for each Lease, each of which was modified by a letter
dated August 19, 2011, agreed to by Great Lakes and RACC, which provides the
date of termination for each Lease. Great Lakes acknowledges its receipt of, and
the correctness in all respects and effectiveness of, such amended Notices of
Terminations and hereby confirms and ratifies each of its obligations under the
Leases. Except for such confirmation and ratification and the provisions of
Sections 2 and 4 of this Agreement, this Agreement does not affect the Leases in
any way, all of which shall remain in full force and effect, subject, however,
to the above-described amended Notices of Termination.

(b) Senior Note. Great Lakes currently is obligated to RACC under a Senior Note
dated March 23, 2007 (the “Senior Note”) that is secured by four (4) Aircraft
Security Agreements, (the “Embraer Security Agreements” and, collectively with
the Senior Note, the “Senior Note Documents”), each of which relates to an
Embraer Model EMB-120ER aircraft. Great Lakes acknowledges its obligations under
the Senior Note Documents and hereby confirms and ratifies each of its
obligations under the Senior Note Documents. Except for such confirmation and
ratification and the provisions of Sections 2 and 4 of this Agreement, this
Agreement does not affect the Senior Note Documents in any way, each of which
shall remain in full force and effect.

4. Other Agreements and General Provisions.

4.1 Information To Be Provided; Co-operation; Etc. Great Lakes agrees to
continue to make business and financial information available to RACC on a
timely basis, consistent with the reports and information provided previously by
Great Lakes to RACC. Great Lakes also agrees to advise RACC as soon as
practicable regarding any business or financial development that Great Lakes
reasonably believes is material to its operations or its refinancing efforts. In
addition, Great Lakes agrees to reasonably co-operate with any actual or
potential transferee of any or all of RACC’s rights or interests in Great Lakes,
including, without limitation, under or in connection with the GLUX/RACC
Documents.

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4.2 Documentation and Filings; Costs; Etc. To the extent that RACC, in its sole
discretion, determines that this Agreement or any provision hereof or for any
other reason, or in connection with any transfer of any of RACC’s rights or
interests in Great Lakes, including, without limitation, under or in connection
with the GLUX/RACC Documents, requires or makes appropriate additional
documentation or filings with any state, federal or international authority or
registry, including, without limitation, the Cape Town International Registry,
RACC is authorized to do so on its own behalf and, as may be reasonably
necessary in RACC’s sole discretion, on behalf of Great Lakes and Great Lakes
hereby consents to any and all such filings. Notwithstanding the right of RACC
to effect any or all such filings without Great Lakes’ participation, Great
Lakes agrees to cooperate with RACC in preparing and effecting any filings. In
addition, by not later than the fifth (5th) business day after the date hereof,
Great Lakes shall file with the Securities and Exchange Commission any necessary
amendment to its registration statement on Form S-1 (File No. 333159256), as may
be necessary to continue the ability of RACC to sell under the registration
statement. All of RACC’s reasonable costs and expenses for preparing this
Agreement, any filings or other matters involving this Agreement shall be paid
by Great Lakes on the date hereof or, if later invoiced, not later than five
(5) days after Great Lakes’ initial receipt thereof

4.3 [Intentionally omitted.]

4.4 Governing Law, Jurisdiction and Venue and Informed Choice. THIS AGREEMENT
WAS MADE AND ENTERED INTO IN THE STATE OF KANSAS AND THE LAW GOVERNING THIS
TRANSACTION SHALL BE THAT OF THE STATE OF KANSAS AS IT MAY FROM TIME TO TIME
EXIST. THE LAWS OF THE STATE OF KANSAS SHALL APPLY TO ANY AND ALL MATTERS
ARISING FROM OR RELATED TO THIS AGREEMENT. THE PARTIES AGREE THAT ANY LEGAL
PROCEEDING BASED UPON THE PROVISIONS OF THIS AGREEMENT SHALL BE BROUGHT
EXCLUSIVELY IN EITHER THE UNITED STATES DISTRICT COURT FOR THE DISTRICT OF
KANSAS AT WICHITA, KANSAS OR IN THE EIGHTEENTH JUDICIAL DISTRICT COURT OF
SEDGWICK COUNTY, KANSAS TO THE EXCLUSION OF ALL OTHER COURTS AND TRIBUNALS.
NOTWITHSTANDING THE ABOVE, RACC, AT ITS SOLE OPTION, MAY INSTITUTE A LEGAL
PROCEEDING IN ANY JURISDICTION AS MAY BE APPROPRIATE IN ORDER FOR RACC TO OBTAIN
POSSESSION OF ANY PROPERTY OR ASSETS IN WHICH RACC HAS, OR MAY CLAIM, ANY RIGHT
OR INTEREST INVOLVING OR RELATED TO GREAT LAKES. THE PARTIES CONSENT AND AGREE
TO BE SUBJECT TO THE JURISDICTION OF THE AFORESAID COURTS IN SUCH PROCEEDING.
EACH PARTY IRREVOCABLY WAIVES ANY OBJECTION, INCLUDING ANY OBJECTION TO THE
LAYING OF VENUE OR BASED ON THE GROUNDS OF FORUM NON CONVENIENS, WHICH IT MAY
NOW OR HEREAFTER HAVE TO THE BRINGING OF ANY ACTION OR PROCEEDING IN SUCH
JURISDICTION IN RESPECT OF THIS AGREEMENT, THE FINANCE DOCUMENTS, THE LEASES,
THE SENIOR LOAN DOCUMENTS OR ANY OTHER DOCUMENT RELATED THERETO. EACH PARTY
WAIVES PERSONAL SERVICE OF ANY SUMMONS, COMPLAINT OR OTHER PROCESS, WHICH MAY BE
MADE BY ANY OTHER MEANS PERMITTED BY THE LAW OF SUCH APPLICABLE STATE.

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4.5 WAIVER OF JURY TRIAL. EACH PARTY TO THIS AGREEMENT WAIVES TRIAL BY JURY IN
ANY ACTION ARISING OUT OF, CONCERNING OR OTHERWISE INVOLVING THIS AGREEMENT.

4.6 Successors and Assigns. This Agreement shall be binding upon and inure to
the benefit of Great Lakes and RACC and their respective successors and assigns,
provided that RACC, but not Great Lakes, may transfer or assign any or all of
its rights, interests, duties or obligations hereunder or under any of the
GLUX/RACC Documents and, in connection with any such transfer or assignment,
Great Lakes hereby consents to such transfers and memorializing such transfers
by filings as contemplated by Section 4.2 of this Agreement

4.7 Counterparts; Execution. This Agreement may be executed in any number of
counterparts, but all such counterparts shall together constitute but one and
the same agreement. In making proof of this Agreement, it shall not be necessary
to produce or account for more than one counterpart thereof signed by each of
the parties hereto. Delivery of an executed signature page to this Agreement by
emailed PDF file or facsimile transmission shall be as effective as delivery of
a manually executed counterpart of this Agreement.

4.8 Amendment; Integration. No provision or term of this Agreement may be
amended, modified, revoked, supplemented, waived or otherwise changed except by
a written instrument duly executed by Great Lakes and RACC and expressly
designated as an amendment, supplement or waiver. This Agreement, and the
GLUX/RACC Documents, constitute the entire agreement and understanding between
Great Lakes and RACC and supersedes any and all prior agreements and
understandings, both written and oral, between the parties, with respect to the
subject matter hereof, the GLUX/RACC Documents and the arrangements between
Great Lakes and RACC.

4.9 Severability. If any provision in this Agreement shall be held invalid,
illegal or unenforceable in any jurisdiction, the validity, legality and
enforceability of the remaining provisions of this Agreement shall not be
impaired thereby, nor shall the validity, legality or enforceability of any such
defective provision be in any way affected or impaired in any other
jurisdiction.

4.10 Waiver and Release of Claims and Defenses.

(a) Great Lakes hereby acknowledges, agrees and affirms that neither it nor any
affiliate possesses any claims, defenses, offsets, recoupment, or counterclaims
of any kind or nature against RACC or its affiliates or with respect to any of
the GLUX/RACC Documents or this Agreement or the enforcement thereof
(collectively, the “Claims”), nor do Great Lakes or its affiliates now have
knowledge of any facts that would or might give rise to any Claims. If facts now
exist that would or could give rise to any Claim against RACC or any of its
affiliates or with respect to any of the GLUX/RACC Documents or this Agreement,
or the enforcement thereof, Great Lakes, on its own behalf and on behalf of its
affiliates, hereby unconditionally,

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irrevocably, and unequivocally waives and fully releases any and all such Claims
as if such Claims were the subject of a lawsuit, adjudicated to final judgment
from which no appeal could be taken, and therein dismissed with prejudice. In no
event shall RACC or its affiliates be liable to Great Lakes or its affiliates,
and Great Lakes, on its own behalf and on behalf of its affiliates, hereby
waives, releases and agrees not to sue for any special, indirect, punitive,
exemplary, or consequential damages suffered by Great Lakes or its affiliates in
connection with, or arising out of, or in any way related to any of the
GLUX/RACC Documents or this Agreement, including without limitation lost
profits, whatever the nature of a breach by RACC or its affiliates of any of
their obligations under any of the GLUX/RACC Documents or this Agreement, and
Great Lakes and RACC, each on its own behalf and on behalf of its affiliates,
hereby waives all claims for special, indirect, punitive, exemplary, or
consequential damages.

(b) Great Lakes, on its own behalf and on behalf of its affiliates hereby
agrees, represents and warrants to RACC and its affiliates that Great Lakes for
its own behalf and on behalf of its affiliates realizes and acknowledges that
factual matters now unknown may have given or may hereafter give rise to causes
of action, claims, demands, debts, controversies, damages, costs, losses and
expenses which are presently unknown, unanticipated and unsuspected, and Great
Lakes, on its own behalf and on behalf of its affiliates, further agrees,
represents and warrants that the release provided hereunder has been negotiated
and agreed upon in light of that realization and that Great Lakes, on its own
behalf and on behalf of its affiliates, nevertheless hereby intends to, and
does, release, discharge and acquit RACC and its affiliates from any such
unknown causes of action, claims, demands, debts, controversies, damages, costs,
losses and expenses which are in any manner set forth in or related to any of
the GLUXIRACC Documents or this Agreement and all dealings in connection
therewith.

4.11 Acknowledgment. By its execution of this Agreement, Great Lakes hereby
ratifies and confirms in all respects all of its obligations to RACC under or in
connection with each of the GLUXIRACC Documents and agrees that they remain in
full force and effect (subject to the terms hereof) and no defenses exist to
RACC’s enforcement thereof. Great Lakes acknowledges and agrees that nothing
contained herein shall constitute a waiver of any default or Event of Default
(as defined in any of the GLUXIRACC Documents) that exists or might occur under
any of the GLUXIRACC Documents or the payment of any amount or the satisfaction
of any obligation except as, and to the extent, expressly so provided herein.

4.12 Time of the Essence. The parties hereto agree that for all purposes under
any of the GLUX/RACC Documents or this Agreement that time is of the essence for
the performance and the accomplishment of each obligation under any of the
foregoing.

4.13 Disclosure of this Agreement. Each party agrees that the other party and/or
its respective affiliates may disclose this Agreement as may be required under
applicable securities laws and as the disclosing party may otherwise, in the
exercise of its commercially reasonable judgment, determine to be necessary or
appropriate for proper commercial purposes.

[SIGNATURE PAGE TO FOLLOW]

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GREAT LAKES:     GREAT LAKES AVIATION, LTD.     By:     /s/    Michael O.
Matthews               Name: Michael O. Matthews       Title: Chief Financial
Officer RACC:     RAYTHEON AIRCRAFT CREDIT CORPORATION     By:   /s/    David A.
Williams       David A. Williams,       Vice President — General Counsel

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Exhibit A

To Second Amendment to Agreement

Model: Beechcraft 1900D Airliner

Manufacturer’s Serial No.:             -            

Aircraft Registration No.: N            

THIRD AMENDMENT TO

[SECOND] AMENDED AND RESTATED PROMISSORY NOTE

Effective this 14th day of October, 2011, this Third Amendment to the [Second]
Amended and Restated Promissory Note (this “Amendment”) is made and entered into
by and between RAYTHEON AIRCRAFT CREDIT CORPORATION (hereinafter, together with
its successors and assigns, “RACC”) and GREAT LAKES AVIATION, LTD. (hereinafter
“Debtor”).

WHEREAS, on or about March 23, 2007, the parties entered into that certain
[Second] Amended and Restated Promissory Note pertaining to the above-identified
Aircraft (as amended and currently in effect, the “Promissory Note”), to which
was attached a Schedule 1, Aircraft Note Payment and Amortization Schedule,
containing a payment schedule as provided in Section 3 of the Promissory Note;

WHEREAS, the parties have reached an agreement to further amend Section_ 3 of
the Promissory Note and, in some respects, the related Payment Schedule and to
extend from October 17, 2011 to November 17, 2011 the date by which Debtor
agrees to pay in full all amounts due under the Promissory Note; and

WHEREAS, the parties desire to enter into this Amendment in order to memorialize
their agreement,

NOW, THEREFORE, for and in consideration of the mutual promises, covenants and
agreements set forth herein and in the Promissory Note, the sufficiency and
receipt of which are hereby acknowledged, the parties agree as follows:

 

  1. Capitalized Terms: Unless otherwise defined herein, the capitalized terms
as used in this Amendment shall have the meanings ascribed to them in the
Promissory Note.

 

  2. Amendment to Section 3: Section 3 of the Promissory Note is hereby amended
to read as follows:

Payment Schedule: Payment of the principal balance together with accrued
interest shall be made in monthly installments payable in arrears, until
November 17, 2011, when Debtor shall pay all unpaid amounts in full. The first
installment payment shall be due and payable to RACC on March 30, 2007. Each
subsequent installment payment shall be due and payable to RACC on the 30th day
of each month thereafter, until November 17, 2011, on which date the entire
remaining balance of principal, accrued interest and any and all other amounts
outstanding and unpaid under or in respect of the Promissory Note shall be due
and payable in full to RACC. The amount of each

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  installment payment will be as set forth on Schedule 1 hereto. Notwithstanding
the foregoing, in the event of loss, theft, confiscation or substantial damage
to the Aircraft, Debtor shall pay all amounts owing under this Promissory Note
upon the earlier of (i) thirty (30) days following demand by RACC or (ii) the
date on which all amounts first become due and payable under the Promissory
Note, whether at maturity, after acceleration or otherwise.

 

  3. Amendment to Schedule 1 to Promissory Note: Schedule 1 to the Promissory
Note, entitled Aircraft Note Payment and Amortization Schedule, is hereby
amended by deleting the last three (3) payments, that is, the payments
designated as Payment # “55”, “56” and “Balloon” thereon, and inserting in lieu
thereof the three (3) payments contained on Exhibit A, which is attached to this
Amendment.

 

  4. Ratification: Except as specifically provided herein, each party hereby
ratifies the other terms and conditions of the Promissory Note, including all
prior amendments thereto, and Debtor hereby confirms and ratifies each of its
obligations under the Promissory Note as modified by this Amendment.

 

  5. Miscellaneous: This Amendment, the Promissory Note and related security,
collateral and other executed agreements between RACC and Debtor contain the
entire agreement of the parties with respect to the subject matter hereof. There
are no oral understandings, agreements, representations or warranties between
the parties that are not expressly set forth in this Amendment and the
Promissory Note or the other documents executed by and between RACC and Debtor.
This Amendment may be executed in counterparts, each of which shall constitute
an original, but all of which when taken together shall constitute a single
document. Delivery of an executed signature page to this Amendment by emailed
PDF file or facsimile transmission shall be as effective as delivery of a
manually executed counterpart of this Amendment. RACC, but not the Debtor, may
transfer or assign any or all of its rights under the Promissory Note and this
Amendment. Time is of the essence for all purposes of the Promissory Note and
this Amendment, including, without limitation, for the performance and the
accomplishment of each of Debtor’s obligations.

IN WITNESS OF THE FOREGOING, the parties have caused their duly authorized
officers to execute and deliver this Amendment under seal effective as of the
date first written above.

 

RAYTHEON AIRCRAFT CREDIT

CORPORATION

    GREAT LAKES AVIATION, LTD. By:           By:        

David A. Williams

Vice President — General Counsel

     

Michael Matthews

Chief Financial Officer

                  “RACC”                       “Debtor”

 

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Exhibit A, Amending Schedule 1

 

Payment #

 

Date

 

Payment

 

Interest

 

Principal

 

Loan Balance

55   9/30/2011   27,600.00   9,262.56   18,337.44   1,251,957.19 56   10/30/2011
  27,600.00   9,685.06   17,914.94   1,234,042.25 Balloon   11/17/2011  
1,239,741.13   5,698.88   1,234,042.25   0.00

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Exhibit B

To Second Amendment to Agreement

FOURTH AMENDMENT TO SECURITY AGREEMENTS

This FOURTH AMENDMENT TO SECURITY AGREEMENTS is made and entered into this 14th
day of October, 2011 (this “Fourth Amendment”), by and between Raytheon Aircraft
Credit Corporation (the “Secured Party”) and Great Lakes Aviation, Ltd. (the
“Debtor”).

W1TNESSETH:

WHEREAS, Debtor and Secured Party have entered into a Second Amendment To
Agreement dated as of the date hereof (the “Second Amendment”), which is an
amendment to an Agreement dated as of June 10, 2011, as amended by an Amendment
To Agreement dated as of August 31, 2011 (collectively, the “2011 Agreement”),
to further extend the final payment date of each of the twenty-five
(25) separate Amended and Restated Promissory Notes or Second Amended and
Restated Promissory Notes, each of which is dated March 23, 2007, issued by
Debtor to Secured Party (each, as originally executed, as amended and currently
in effect, a “Promissory Note” and collectively, the “Promissory Notes”) in
connection with that certain Amended and Restated Restructuring Agreement dated
as of March 9, 2007 (the “2007 Restructuring Agreement”);

WHEREAS, in connection with the 2007 Restructuring Agreement and to further
secure the Promissory Notes, Debtor provided Secured Party with twenty-five
(25) separate First Amendments, dated as of March 23, 2007, a Second Amendment
to Security Agreements, dated June 10, 2011, and a Third Amendment to Security
Agreements dated August 31, 2011, to twenty-five (25) Security Agreements or
Amended and Restated Security Agreements, each of which is dated as of
December 31, 2002, all as further described in Exhibit A attached hereto
(collectively the “Original Security Agreements”);

WHEREAS, in addition to the Original Security Agreements, Debtor and Secured
Party entered into that Security Agreement dated as of May 1, 2008, as recorded
by the Federal Aviation Administration (“FAA”) on June 12, 2008 as Conveyance
No. LA000196; and as supplemented by that certain Security Agreement Supplement
No. I dated May 27, 2009, between Debtor and Secured Party, recorded by the FAA
on June 10, 2009 as Conveyance No. SF002448, and supplemented by that certain
Security Agreement Supplement No. 2 dated January 27, 2010, between Debtor and
Secured Party, recorded by the FAA on February 23, 2010 as Conveyance No.
MS003073, and supplemented by that certain Security Agreement Supplement No. 3
dated April 15, 2010, between Debtor and Secured Party, recorded by the FAA on
May 4, 2010 as Conveyance No. MC006524, and supplemented by that certain
Security Agreement Supplement No. 4 dated October 27, 2010, between Debtor and
Secured Party, recorded by the FAA on November 22, 2010 as Conveyance No.
WH002898, and further supplemented by that certain Security Agreement Supplement
No. 5 dated April 25, 2011, between Debtor and Secured Party, recorded by the
FAA on May 25, 2011 as Conveyance No. DV010100, and further supplemented by that
certain Security Agreement Supplement No. 6 dated August 25, 2011, between
Debtor and Secured Party, recorded by the FAA on September

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26, 2011 as Conveyance No. DP002952 (collectively, the “2008 Security Agreement”
and, the 2008 Security Agreement and the Original Security Agreements, as they
are being amended hereby and as they are amended from time to time. are
hereinafter referred to as the “Security Agreements”);

WHEREAS, Debtor previously has amended the Promissory Notes and on or about the
date hereof is further amending the Promissory Notes by executing twenty-five
(25) separate Third Amendments to the Amended and Restated Promissory Notes or
Third Amendments to Second Amended and Restated Promissory Notes, each of which
is dated on the date hereof, to further amend the Promissory Notes (as so
amended, the “Amended Promissory Notes”) to reflect new installment payments and
a modified final due date, all as provided in the Second Amendment; and

WHEREAS, Debtor and Secured Party wish to execute this Fourth Amendment to
reflect that (i) the references in the Security Agreements to the “Restructuring
Agreement” are to the 2007 Restructuring Agreement, the 2011 Agreement and the
Second Amendment, (ii) the references in the Security Agreements to the
“Promissory Note” are to the Amended Promissory Notes, and (iii) the Original
Security Agreements and the 2008 Security Agreement continue to secure all of
the obligations of Debtor to Secured Party.

NOW THEREFORE, in consideration of the premises and other good and valuable
consideration, receipt of which is hereby acknowledged, Debtor and Secured Party
hereby agree as follows:

 

  1. Unless otherwise defined herein, the capitalized terms as used in this
Fourth Amendment shall have the meaning assigned to them in the Security
Agreements.

 

  2. The definition of the Promissory Note in the Security Agreements is hereby
amended to mean the Amended Promissory Notes, as they may be further amended,
modified, extended or amended and restated and in effect from time to time.

 

  3. The definition of the “Restructuring Agreement” in the Security Agreements
is hereby amended to mean the 2007 Restructuring Agreement, the 2011 Agreement
and the Second Amendment, as they may be amended, modified, extended or amended
and restated and in effect from time to time.

 

  4. Regarding the Cape Town Treaty, (a) Debtor shall establish a valid and
existing account with the International Registry, appoint an Administrator
and/or a Professional User acceptable to Secured Party to make registration in
regards to the Collateral and Additional Collateral identified in the Security
Agreements as may be requested by Secured Party, and (b) Secured Party and
Debtor shall register a first priority Prospective International Interest in
connection with the Collateral and Additional Collateral identified in each of
the Security Agreements as may be requested by Secured Party which shall be
perfected and searchable in the International Registry to the satisfaction of
Secured Party.

 

  5.

Secured Party may transfer or assign all or any part of its interest in the
Security Agreements, as amended and further supplemented, without the consent of
Debtor or any

--------------------------------------------------------------------------------

  other party. Debtor hereby consents to any and all assignments or sales of, or
the granting of participations in this Fourth Amendment by Secured Party or any
assignee of an interest in the Security Agreements. Debtor shall not assign,
transfer, encumber or convey any of its interests in the Collateral, Additional
Collateral or in the Security Agreements without the prior written consent of
Secured Party.

 

  6. Unless amended by the terms and conditions of this Fourth Amendment, the
parties hereby (i) ratify all remaining terms and conditions of the Security
Agreements as if the same were restated herein (and without limitation as a
precautionary matter, the Debtor hereby re-grants to Secured Party a security
interest in the Collateral and Additional Collateral subject to the Security
Agreements and under the terms of the Security Agreements), and (ii) confirm
that the Security Agreements otherwise remain in full force and effect as to any
and all collateral subject thereto.

 

  7. GOVERNING LAW AND FORUM SELECTION. THIS FOURTH AMENDMENT SHALL BE GOVERNED
BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF KANSAS. ANY LEGAL
PROCEEDINGS RELATING TO THIS FOURTH AMENDMENT SHALL BE BROUGHT IN THE EIGHTEENTH
JUDICIAL DISTRICT AT WICHITA, KANSAS, OR THE UNITED STATES DISTRICT COURT FOR
THE DISTRICT OF KANSAS AT WICHITA, KANSAS, TO THE EXCLUSION OF ALL OTHER COURTS
AND TRIBUNALS. NOTWITHSTANDING THE ABOVE, SECURED PARTY (AT ITS SOLE OPTION) MAY
INSTITUTE A LEGAL PROCEEDING IN ANY JURISDICTION AS MAY BE APPROPRIATE IN ORDER
FOR SECURED PARTY TO EXERCISE ITS RIGHTS AND REMEDIES UNDER THIS FOURTH
AMENDMENT. THE PARTIES HEREBY IRREVOCABLY CONSENT AND AGREE TO BE SUBJECT TO THE
JURISDICTION OF THE AFORESAID COURTS IN SUCH PROCEEDINGS.

 

  8. This Fourth Amendment and the other written agreements entered into by the
parties hereto constitute the entire agreement by and between the parties with
respect to the subject matter hereof. There are no oral understandings,
agreements, representations or warranties not expressly set forth in this Fourth
Amendment or the other written agreements between the parties hereto. Neither
this Fourth Amendment nor the Security Agreements shall be changed orally, but
only by writing signed by the parties. This Fourth Amendment may be executed in
any number of counterparts, but all such counterparts shall together constitute
but one and the same agreement. In making proof of this Fourth Amendment, it
shall not be necessary to produce or account for more than one counterpart
thereof signed by each of the parties hereto. Delivery of an executed signature
page to this Fourth Amendment by emailed PDF file or facsimile transmission
shall be as effective as delivery of a manually executed counterpart of this
Fourth Amendment.

--------------------------------------------------------------------------------

IN WITNESS WHEREOF, the undersigned have duly executed and delivered this Fourth
Amendment under seal as of the date first set forth above.

GREAT LAKES AVIATION, LTD., Debtor By:     Name:     Title:    
RAYTHEON AIRCRAFT CREDIT CORPORATION,
Secured Party By:     Name:   David A. Williams Title:   Vice President —
General Counsel

--------------------------------------------------------------------------------

EXHIBIT “A”

To Fourth Amendment to Security Agreements

Security Agreement UE-100

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, (“Great Lakes”) as debtor, and Raytheon Aircraft Credit Corporation
(“RACC”), as secured party, recorded by the Federal Aviation Administration (the
“FAA”) on March 10, 2003, as Conveyance Number T071645, and amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number Q079643, as further amended by the
Second Amendment to the Security Agreements dated as of June 10, 2011 (the
“Second Amendment”), between Great Lakes, as debtor, and RACC, as secured party,
recorded by the FAA on September 19, 2011, as Conveyance Number AB003879, and as
further amended by the Third Amendment to the Security Agreements dated as of
August 31, 2011 (the “Third Amendment”), between Great Lakes, as debtor, and
RACC, as secured party, recorded by the FAA on September 19, 2011, as Conveyance
No. AB003881.

Security Agreement UE-122

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 20, 2003, as Conveyance Number JJ000799, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number PP036045, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-153

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
March 10, 2003, as Conveyance Number T071657, as amended by the First Amendment
to Amended and Restated Security Agreement dated as of March 23, 2007, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
September 12, 2007, as Conveyance Number FF008509, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-154

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 20, 2003, as Conveyance Number JJ000800, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number PP036046, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-169

Security Agreement dated as of December 31, 2002, between Great Lakes, as
debtor, and RACC, as secured party, recorded by the FAA on February 20, 2003, as
Conveyance Number JJ000807, as amended by the First Amendment to Security
Agreement dated as of March 23, 2007, between

--------------------------------------------------------------------------------

Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
September 19, 2007, as Conveyance Number PP036047, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-170

Security Agreement dated as of December 31, 2002, between Great Lakes, as
debtor, and RACC, as secured party, recorded by the FAA on February 24, 2003, as
Conveyance Number QQ026578, as amended by the First Amendment to Security
Agreement dated as of March 23, 2007, by Great Lakes, as debtor, and RACC, as
secured party, recorded by the FAA on September 18, 2007, as Conveyance Number
K043465, as further amended by the Second Amendment, and as further amended by
the Third Amendment.

Security Agreement UE-184

Amended and Restated Security Agreement dated December 31, 2002 with Great
Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 21, 2003, as Conveyance Number QQ026561, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 26, 2007, as Conveyance Number HH045092, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-192

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 27, 2003, as Conveyance Number T071584, as amended by the First
Amendment to Amended and Restated and Restated Security Agreement dated as of
March 23, 2007, between Great Lakes, as debtor, and RACC, as secured party,
recorded by the FAA on September 21, 2007, as Conveyance Number W008675, as
further amended by the Second Amendment, and as further amended by the Third
Amendment.

Security Agreement UE-195

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 20, 2003, as Conveyance Number QQ026557, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 21, 2007, as Conveyance Number W008675, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-201

Security Agreement dated as of December 31, 2002, between Great Lakes, as
debtor, and RACC, as secured party, recorded by the FAA on March 10, 2003, as
Conveyance Number T071656, as amended by the First Amendment to Security
Agreement dated as of March 23, 2007, between Great Lakes, as debtor, and RACC,
as secured party, recorded by the FAA on September 19, 2007, as Conveyance
Number PP036048, as further amended by the Second Amendment, and as further
amended by the Third Amendment.

 

B-2

--------------------------------------------------------------------------------

Security Agreement UE-202

Security Agreement with. dated as of December 31, 2002, between Great Lakes, as
debtor, and RACC, as secured party, recorded by the FAA on March 3, 2003, as
Conveyance Number T071592, as amended by the First Amendment to Security
Agreement dated as of March 23, 2007, between Great Lakes, as debtor, and RACC,
as secured party, recorded by the FAA on September 19, 2007, as Conveyance
Number PP036058, as further amended by the Second Amendment, and as further
amended by the Third Amendment.

Security Agreement UE-208

Security Agreement dated as of December 31, 2002, between Great Lakes, as
debtor, and RACC, as secured party, recorded by the FAA on March 4, 2003, as
Conveyance Number T071604; as amended by the First Amendment to Security
Agreement dated as of March 23, 2007, between Great Lakes, as debtor, and RACC,
as secured party, recorded by the FAA on September 21, 2007, as Conveyance
Number PP036059, as further amended by the Second Amendment, and as further
amended by the Third Amendment.

Security Agreement UE-210

Security Agreement dated as of December 31, 2002 between Great Lakes, as debtor,
and RACC, as secured party, recorded by the FAA on March 3, 2003, as Conveyance
Number T071598, as amended by the First Amendment to Security Agreement dated as
of March 23, 2007, between Great Lakes, as debtor, and RACC, as secured party,
recorded by the FAA on September 19, 2007, as Conveyance Number PP036061, as
further amended by the Second Amendment, and as further amended by the Third
Amendment.

Security Agreement UE-211

Security Agreement dated as of December 31, 2002 between Great Lakes, as debtor,
and RACC, as secured party, recorded by the FAA on February 21, 2003, as
Conveyance Number JJ000830, as amended by the First Amendment to Security
Agreement dated as of March 23, 2007 between Great Lakes, as debtor, and RACC,
as secured party, recorded by the FAA on September 21, 2007, as Conveyance
Number PP036062, as further amended by the Second Amendment, and as further
amended by the Third Amendment.

Security Agreement UE-219

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 25, 2003, and assigned Conveyance Number JJ000836, as amended by the
First Amendment to Amended and Restated Security Agreement dated as of March 23,
2007, between Great Lakes, as debtor, and RACC, as secured party, recorded by
the FAA on September 19, 2007, as Conveyance Number K043466, as further amended
by the Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-220

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 25, 2003, as Conveyance Number T071538, as amended by the First
Amendment to Amended and Restated Security

 

B-3

--------------------------------------------------------------------------------

Agreement dated as of March 23, 2007, between Great Lakes, as debtor, and RACC,
as secured party, recorded by the FAA on September 21, 2007, as Conveyance
Number PP036060, as further amended by the Second Amendment, and as further
amended by the Third Amendment.

Security Agreement UE-240

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 25, 2003, as Conveyance Number T071540, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 21, 2007, as Conveyance Number K043471, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-245

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 26, 2003, as Conveyance Number T071578, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number K043468, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-247

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 21, 2003, as Conveyance Number QQ026565, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number K043469, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-251

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 27, 2003, as Conveyance Number T071580, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number K043470, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-253

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 27, 2003, as Conveyance Number T071582, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number K043467, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

 

B-4

--------------------------------------------------------------------------------

Security Agreement UE-254

Security Agreement dated as of December 31, 2002, between Great Lakes, as
debtor, and RACC, as secured party, recorded by the FAA on February 20, 2003, as
Conveyance Number JJ000815, as amended by the First Amendment to Security
Agreement dated as of March 23, 2007, between Great Lakes Aviation, Ltd. as
debtor, and RACC, as secured party, recorded by the FAA on September 21, 2007,
as Conveyance Number K043473, as further amended by the Second Amendment, and as
further amended by the Third Amendment.

Security Agreement UE-255

Security Agreement dated as of December 31, 2002, between Great Lakes, as
debtor, and RACC, as secured party, recorded by the FAA on February 20, 2003, as
Conveyance Number JJ000823, as amended by the First Amendment to Security
Agreement dated as of March 23, 2007, between Great Lakes, as debtor, and RACC,
as secured party, recorded by the FAA on September 21, 2007, as Conveyance
Number K043472as further amended by the Second Amendment, and as further amended
by the Third Amendment.

Security Agreement UE-257

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 24, 2003, as Conveyance Number JJ000832, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 19, 2007, as Conveyance Number PP036044, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

Security Agreement UE-261

Amended and Restated Security Agreement dated as of December 31, 2002, between
Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA on
February 25, 2003, as Conveyance Number JJ000838, as amended by the First
Amendment to Amended and Restated Security Agreement dated as of March 23, 2007,
between Great Lakes, as debtor, and RACC, as secured party, recorded by the FAA
on September 21, 2007, as Conveyance Number K043474, as further amended by the
Second Amendment, and as further amended by the Third Amendment.

 

B-5

--------------------------------------------------------------------------------

Exhibit C

To Second Amendment to Agreement

Identification of Operating Leases

 

  1. Used Beech 1900D Airliner Operating Lease Agreement Pertaining to Aircraft
Serial No. UE-231 Dated December 17, 2008

 

  2. Used Beech 1900D Airliner Operating Lease Agreement Pertaining to Aircraft
Serial No. UE-182 Dated February 2, 2009

 

  3. Used Beech 1900D Airliner Operating Lease Agreement Pertaining to Aircraft
Serial No. UE-165 Dated April 9, 2009

 

B-6