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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549





FORM 10-K/A

(Amendment No. 1)





(Mark One)

|x | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------

For the Fiscal Year Ended December 31, 2012

OR



| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transition period from
 to

Commission File Number: 001-35232





WAGEWORKS, INC.

(Exact name of Registrant as specified in its charter)







|                                                               |  |                                     
|-------------------------------------------------------------- |  | ------------------------------------
|Delaware                                                       |  | 94-3351864                          
|(State or other jurisdiction of
incorporation or organization) |  | (I.R.S. Employer Identification No.)



|                                         |  |           
|---------------------------------------- |  | ----------
|1100 Park Place, 4th Floor               |  |           
|San Mateo, California                    |  | 94403     
|(Address of principal executive offices) |  | (Zip Code)

(650) 577-5200

(Registrants telephone number, including area code)

Securities
registered pursuant to Section 12(b) of the Act:





|                               |  |                                          
|------------------------------ |  | -----------------------------------------
|Title of each class            |  | Name of each exchange on which registered
|Common Stock, $0.001 par value |  | The New York Stock Exchange              

Securities registered pursuant to Section 12(g) of the Act:

None.





Indicate by check mark if the
registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities
Act.    Yes   ̈    No  x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes   ̈    No  x

Indicate by
check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to
file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No   ̈

Indicate by check mark whether the registrant has submitted electronically and posted to its
corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such
files).    Yes  x    No   ̈

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrants knowledge, in
definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.     ̈

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company.
See the definitions of large accelerated filer, accelerated filer and smaller reporting company in Rule 12b-2 of the Exchange Act.



|                        |  |                                                  |  |                           |  |  
|----------------------- |  | ------------------------------------------------ |  | ------------------------- |  | -
|Large accelerated filer |  |  ̈                                                |  | Accelerated filer         |  |  ̈
|                        |  |                                                  | 
|Non-accelerated filer   |  | x  (Do not check if a smaller reporting company) |  | Smaller reporting company |  |  ̈

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange
Act).    Yes   ̈    No  x

The aggregate market value of the registrants common stock, $0.001 par value per share, held by non-affiliates of the registrant on June 29, 2012, the last business day of the registrants
most recently completed second fiscal quarter, was $144,698,814 (based on the closing sales price of the registrants common stock on that date). This determination of affiliate status is not necessarily a conclusive determination for other
purposes.

As of February 20, 2013, there were 32,175,608 shares of the registrants common stock outstanding.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of the registrants Proxy Statement for its 2013 Annual Meeting of the Stockholders (the 2013 Proxy Statement), to be filed with the Securities and Exchange Commission not later
than 120 days after the end of the year covered by this Annual Report, are incorporated by reference into Part III of this Annual Report where indicated.









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WAGEWORKS, INC.

FORM 10-K/A

Table of Contents



|                                                    |  |  |   | 
|--------------------------------------------------- |  |  | - | 
|PART IV                                             | 
|                                                    | 
|Item 15. Exhibits and Financial Statement Schedules |  |  | 1 | 
|Signatures                                          |  |  | 2 | 



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EXPLANATORY NOTE

We are filing this Amendment No. 1 on Form 10-K/A (this Amendment) to our Annual Report on Form 10-K for the period ended
December 31, 2012 (the Original Filing), which was originally filed with the U.S. Securities and Exchange Commission (the SEC) on February 27, 2013, solely to re-file Exhibits 10.26 and 10.27 for which we are no longer
seeking confidential treatment from the SEC.

This Amendment does not reflect events occurring after the filing of the
Original Filing. No other modifications or changes have been made to the Original Filing or the exhibits filed therewith. Accordingly, this Amendment should be read in conjunction with the Original Filing and our other filings with the SEC.



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PART IV.

Item 15. Exhibits and Financial Statement Schedules



| | 3. | Exhibits:
| | -- | ---------

The documents listed
in the Exhibit Index of this Annual Report on Form 10-K are incorporated by reference or are filed with this report, in each case as indicated therein (numbered in accordance with Item 601 of Regulation S-K).



1



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SIGNATURES

Pursuant to the requirements of Sections 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized.



|                     |  |     |  |                                             
|-------------------- |  | --- |  | --------------------------------------------
|                     |  |     |  | WAGEWORKS, INC.                             
|                     |  |    
|Date: March 11, 2013 |  | By: |  | /s/ Richard T. Green                        
|                     |  |     |  | Richard T. Green                            
|                     |  |     |  | Chief Financial Officer                     
|                     |  |     |  | (Principal Financial and Accounting Officer)



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|               |  |                                                                                                                                     |  |                           |  |            |  |  |             |  |  |           
|-------------- |  | ----------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- |  | ---------- |  |  | ----------- |  |  | ----------
|Exhibit
Number |  | Exhibit Description                                                                                                                 |  | Incorporated by Reference
|               |  | Form                                                                                                                                |  | File No.                  |  | Exhibit    |  |  | Filing Date
|               |  |                                                                                                                                     |  |                           | 
|10.7*          |  | Form of Subscription Agreement under 2012 Employee Stock Purchase Plan                                                              |  | S-1                       |  | 333-173709 |  |  | 10.7        |  |  | 03/07/2012
|               |  |                                                                                                                                     |  |                           | 
|10.8*          |  | Second Amended and Restated Employment Agreement, dated as of November 23, 2010, between Registrant and Joseph L. Jackson           |  | S-1                       |  | 333-173709 |  |  | 10.8        |  |  | 06/08/2011
|               |  |                                                                                                                                     |  |                           | 
|10.9*          |  | Form of Amended and Restated Executive Severance Benefit Agreement Purchase Plan                                                    |  | S-1                       |  | 333-173709 |  |  | 10.9        |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.10          |  | Commercial Credit Agreement, between Registrant and Union Bank, N.A., dated as of August 31, 2010                                   |  | S-1                       |  | 333-173709 |  |  | 10.10       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.10A         |  | First Loan Modification Agreement, by and among Registrant, Union Bank, N.A. and MHM Resources, LLC, dated as of November 16, 2011  |  | S-1                       |  | 333-173709 |  |  | 10.10A      |  |  | 03/07/2012
|               |  |                                                                                                                                     |  |                           | 
|10.10B         |  | Second Loan Modification Agreement, by and among Registrant, Union Bank, N.A. and MHM Resources, LLC, dated as of February 14, 2012 |  | S-1                       |  | 333-173709 |  |  | 10.10B      |  |  | 03/07/2012
|               |  |                                                                                                                                     |  |                           | 
|10.10C         |  | Third Loan Modification Agreement, by and among Registrant, Union Bank, N.A. and MHM Resources, LLC, dated as of September 20, 2012 |  | 8-K                       |  | 001-35232  |  |  | 10.1        |  |  | 09/24/2012
|               |  |                                                                                                                                     |  |                           | 
|10.10D         |  | Fourth Loan Modification Agreement, by and among Registrant, Union Bank, N.A. and MHM Resources, LLC, dated as of December 31, 2012 |  | 10-K                      |  | 001-35232  |  |  | 10.10D      |  |  | 02/27/2013
|               |  |                                                                                                                                     |  |                           | 
|10.11          |  | Sublease Agreement between Oracle USA, Inc. and Registrant, dated as of September 13, 2006                                          |  | S-1                       |  | 333-173709 |  |  | 10.11       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.12          |  | First Amendment to Sublease between Oracle USA, Inc. and Registrant, dated as of October 30, 2006                                   |  | S-1                       |  | 333-173709 |  |  | 10.12       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.13          |  | Commercial Building Lease, by and between Applied Buildings, LLC and HCAP Strategies, Inc., dated as of December 17, 2004           |  | S-1                       |  | 333-173709 |  |  | 10.13       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.14          |  | Assignment and Assumption of Lease, between, HCAP Strategies, Inc. and Registrant, dated as of May 16, 2005                         |  | S-1                       |  | 333-173709 |  |  | 10.14       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.15          |  | Amendment to Commercial Building Lease, between Applied Buildings, LLC and Registrant, dated as of September 8, 2005                |  | S-1                       |  | 333-173709 |  |  | 10.15       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.16          |  | Lease, by and between Phoenix Investors #25, L.L.C. and Registrant, dated as of July 23, 2007                                       |  | S-1                       |  | 333-173709 |  |  | 10.16       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.17          |  | First Amendment to Lease, by and between Phoenix Investors #25, L.L.C. and Registrant, dated as of May 24, 2010                     |  | S-1                       |  | 333-173709 |  |  | 10.17       |  |  | 04/25/2011
|               |  |                                                                                                                                     |  |                           | 
|10.18          |  | Second Amendment to Lease, by and between Phoenix Investors #25, L.L.C. and Registrant, dated as of August 31, 2010                 |  | S-1                       |  | 333-173709 |  |  | 10.18       |  |  | 04/25/2011



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|               |  |                                                                                                                                                                                           |  |                           |  |            |  |             |  |           
|-------------- |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- |  | ---------- |  | ----------- |  | ----------
|Exhibit
Number |  | Exhibit Description                                                                                                                                                                       |  | Incorporated by Reference
|               |  | Form                                                                                                                                                                                      |  | File No.                  |  | Exhibit    |  | Filing Date
|               |  |                                                                                                                                                                                           |  |                           | 
|10.19          |  | Sublease Agreement, dated as of June 1, 2011, by and between Fringe Benefits Management Company and Registrant                                                                            |  | S-1                       |  | 333-173709 |  | 10.19       |  | 06/08/2011
|               |  |                                                                                                                                                                                           |  |                           | 
|10.20          |  | Office Lease between Revere Corporate Center, LLC and Planned Benefits Systems, Inc., dated as of May 3, 2006                                                                             |  | S-1                       |  | 333-173709 |  | 10.20       |  | 04/25/2011
|               |  |                                                                                                                                                                                           |  |                           | 
|10.21          |  | Amendment to Lease Agreement, dated as of October 6, 2008, by and between Revere Corporate Center, LLC and Planned Benefits Systems, Inc.                                                 |  | S-1                       |  | 333-173709 |  | 10.21       |  | 04/25/2011
|               |  |                                                                                                                                                                                           |  |                           | 
|10.22          |  | Pinnacle Corporate Centre IV Standard Office Lease, dated as of February 8, 2008, by and between BK Pinnacle IV LLC and MHM Resources, LLC                                                |  | S-1                       |  | 333-173709 |  | 10.22       |  | 04/25/2011
|               |  |                                                                                                                                                                                           |  |                           | 
|10.23          |  | First Amendment to Lease, dated as of April 30, 2008, by and between BK Pinnacle IV LLC and MHM Resources, LLC                                                                            |  | S-1                       |  | 333-173709 |  | 10.23       |  | 04/25/2011
|               |  |                                                                                                                                                                                           |  |                           | 
|10.24          |  | Second Amendment to Lease dated as of August 12, 2008 by and between BK Pinnacle IV LLC and MHM Resources, LLC                                                                            |  | S-1                       |  | 333-173709 |  | 10.24       |  | 04/25/2011
|               |  |                                                                                                                                                                                           |  |                           | 
|10.25          |  | Second Amendment to Sublease between Oracle America, Inc. and Registrant, dated as of May 1, 2011                                                                                         |  | S-1                       |  | 333-173709 |  | 10.25       |  | 06/08/2011
|               |  |                                                                                                                                                                                           |  |                           | 
|10.26*++       |  | 2011 Bonus Plan                                                                                                                                                                           |  |                           |  |            |  |             |  |           
|               |  |                                                                                                                                                                                           |  |                           | 
|10.27*++       |  | 2012 Bonus Plan                                                                                                                                                                           |  |                           |  |            |  |             |  |           
|               |  |                                                                                                                                                                                           |  |                           | 
|10.28*+        |  | 2013 Bonus Plan                                                                                                                                                                           |  | 10-K                      |  | 001-35232  |  | 10.28       |  | 02/27/2013
|               |  |                                                                                                                                                                                           |  |                           | 
|10.29*         |  | Amended Form of Stock Option Agreement under the Amended and Restated 2010 Equity Incentive Plan                                                                                          |  | 10-K                      |  | 001-35232  |  | 10.29       |  | 02/27/2013
|               |  |                                                                                                                                                                                           |  |                           | 
|10.30*         |  | Form of Restricted Stock Unit Agreement under the Amended and Restated 2010 Equity Incentive Plan                                                                                         |  | 10-K                      |  | 001-35232  |  | 10.30       |  | 02/27/2013
|               |  |                                                                                                                                                                                           |  |                           | 
|21.1           |  | List of subsidiaries of Registrant                                                                                                                                                        |  | S-1                       |  | 333-173709 |  | 21.1        |  | 03/07/2012
|               |  |                                                                                                                                                                                           |  |                           | 
|23.1           |  | Consent of KPMG LLP, Independent Registered Public Accounting Firm                                                                                                                        |  | 10-K                      |  | 001-35232  |  | 23.1        |  | 02/27/2013
|               |  |                                                                                                                                                                                           |  |                           | 
|24.1           |  | Power of Attorney (contained in the signature page to the Annual Report)                                                                                                                  |  | 10-K                      |  | 001-35232  |  | 24.1        |  | 02/27/2013
|               |  |                                                                                                                                                                                           |  |                           | 
|31.1           |  | Certification of the Principal Executive Officer Pursuant to Exchange Act Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of
2002             |  |                           |  |            |  |             |  |           
|               |  |                                                                                                                                                                                           |  |                           | 
|31.2           |  | Certification of the Principal Financial Officer Pursuant to Exchange Act Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of
2002             |  |                           |  |            |  |             |  |           
|               |  |                                                                                                                                                                                           |  |                           | 
|32.1**         |  | Certification of the Principal Executive Officer and Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of
2002 |  | 10-K                      |  | 001-35232  |  | 32.1        |  | 02/27/2013
|               |  |                                                                                                                                                                                           |  |                           | 
|101.INS      |  | XBRL Instance Document                                                                                                                                                                    |  | 10-K                      |  | 001-35232  |  | 101.INS     |  | 02/27/2013



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|               |  |                                               |  |                           |  |           |  |             |  |           
|-------------- |  | --------------------------------------------- |  | ------------------------- |  | --------- |  | ----------- |  | ----------
|Exhibit
Number |  | Exhibit Description                           |  | Incorporated by Reference
|               |  | Form                                          |  | File No.                  |  | Exhibit   |  | Filing Date
|               |  |                                               |  |                           | 
|101.SCH      |  | XBRL Taxonomy Extension Schema                |  | 10-K                      |  | 001-35232 |  | 101.SCH     |  | 02/27/2013
|               |  |                                               |  |                           | 
|101.CAL      |  | XBRL Taxonomy Extension Calculation Linkbase  |  | 10-K                      |  | 001-35232 |  | 101.CAL     |  | 02/27/2013
|               |  |                                               |  |                           | 
|101.DEF      |  | XBRL Taxonomy Extension Definition Linkbase   |  | 10-K                      |  | 001-35232 |  | 101.DEF     |  | 02/27/2013
|               |  |                                               |  |                           | 
|101.LAB      |  | XBRL Taxonomy Extension Label Linkbase        |  | 10-K                      |  | 001-35232 |  | 101.LAB     |  | 02/27/2013
|               |  |                                               |  |                           | 
|101.PRE      |  | XBRL Taxonomy Extension Presentation Linkbase |  | 10-K                      |  | 001-35232 |  | 101.PRE     |  | 02/27/2013



|* | Indicates a management contract or compensatory plan or arrangement.
|- | --------------------------------------------------------------------

|+ | Confidential treatment has been requested for portions of this exhibit. These portions have been omitted and have been filed separately with the Securities and Exchange
Commission.
|- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|++ | This exhibit was originally filed with our Original Filing and is being re-filed as an Exhibit hereto in unredacted form.
|-- | -------------------------------------------------------------------------------------------------------------------------

|** | The certifications attached as Exhibit 32.1 that accompany the Original Filing, are not deemed filed with the Securities and Exchange Commission and are not to be
incorporated by reference into any filing of WageWorks, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date of the Original Filing, irrespective of any general
incorporation language contained in such filing.
|-- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | XBRL (Extensible Business Reporting Language) information is furnished and not filed or a part of a registration statement or prospectus for purposes of Sections 11 or
12 of the Securities Act of 1933, as amended, is deemed not filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and is not otherwise subject to liability under these Sections.
|-- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



5