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

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

|                                                               |
|---------------------------------------------------------------|
|                                                               |  |  |
| Delaware                                                      |   | 04-3387530 |
| (State or other jurisdiction ofincorporation or organization) |   | (I.R.S. EmployerIdentification No.) |
|                                                          |   |
| 311 Arsenal Street,Watertown, Massachusetts                   |   | 02472 |
| (Address of principal executive offices)                      |   | (Zip Code) |

|                                    |
|------------------------------------|
|                                    |  |  |
|                               |   |   |
| Title of each class                |   | Name of each exchange on which registered |
| Common Stock, $0.01 par value |   | The NASDAQ Stock Market LLC |

----

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

|               |
|---------------|
|               |  |
| Item 15. | Exhibits, Financial Statement Schedules. |

----

Table of Contents

|                    |
|--------------------|
|                    |  |  |
|               |   |   |
| ATHENAHEALTH, INC. |
|               |   |
| By:                |   | /s/ Jonathan Bush |
|               |   | Jonathan Bush |
|               |   | Chief Executive Officer, President, and Chairman |
|               |   |
| By:                |   | /s/ Karl A. Stubelis |
|               |   | Karl A. Stubelis |
|               |   | Chief Financial Officer and Senior Vice President |

|        |
|--------|
|        |  |  |  |  |
|   |   |   |   |   |

----

|              |
|--------------|
|              |  |  |  |  |  |  |  |  |  |
| ExhibitNo.   |   | Exhibit Description |   | Incorporated by Reference |   |
|         |   |   | Form |   | File No. |   | Filing Date |   |
| 2.1          |   | Agreement and Plan of Merger by and among the Registrant, Echo Merger Sub, Inc., and Epocrates, Inc., dated January 7, 2013 |   | 8-K |   | 001-33689 |   | January 7, 2013 |   |
|         |   |   |   |   |   |   |   |   |
| 3.1          |   | Amended and Restated Certificate of Incorporation of the Registrant |   | S-1 |   | 333-143998 |   | September 11, 2007 |   |
|         |   |   |   |   |   |   |   |   |
| 3.2          |   | Amended and Restated Bylaws of the Registrant |   | S-1 |   | 333-143998 |   | September 11, 2007 |   |
|         |   |   |   |   |   |   |   |   |
| 4.1          |   | Specimen Certificate evidencing shares of common stock |   | S-1 |   | 333-143998 |   | August 3, 2007 |   |
|         |   |   |   |   |   |   |   |   |
| 10.1         |   | Form of Indemnification Agreement between the Registrant and each of its directors and officers |   | S-1 |   | 333-143998 |   | September 6, 2007 |   |
|         |   |   |   |   |   |   |   |   |
| †10.2  |   | athenahealth, Inc. 2000 Stock Option and Incentive Plan, as amended, and form of agreements |   | S-1 |   | 333-143998 |   | July 13, 2007 |   |
|         |   |   |   |   |   |   |   |   |
| †10.3  |   | athenahealth, Inc. 2007 Stock Option and Incentive Plan, as amended, and form of agreements |   | 10-Q |   | 001-33689 |   | October 18, 2013 |   |
|         |   |   |   |   |   |   |   |   |
| †10.4  |   | athenahealth, Inc. 2007 Employee Stock Purchase Plan, as amended |   | 10-Q |   | 001-33689 |   | October 19, 2012 |   |
|         |   |   |   |   |   |   |   |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.5  |   | Epocrates, Inc. 2010 Equity Incentive Plan, as amended, and form of agreements |   | 10-Q |   | 001-33689 |   | July 18, 2014 |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.6  |   | Employment Agreement by and between the Registrant and Jonathan Bush, dated November 1, 1999, as amended |   | S-1 |   | 333-143998 |   | July 13, 2007 |   |
|         |   |   |   |   |   |   |   |   |
| †10.7  |   | Employment Agreement by and between the Registrant and Stephen Kahane, dated February 18, 2011 |   | 10-Q |   | 001-33689 |   | April 29, 2011 |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.8  |   | Employment Agreement by and between the Registrant and Karl Stubelis, dated May 19, 2016 |   | 8-K |   | 001-33689 |   | May 19, 2016 |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.9  |   | Employment Agreement by and between the Registrant and Ed Park, dated July 1, 2010 |   | 10-Q |   | 001-33689 |   | October 22, 2010 |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.10 |   | Employment Agreement by and between the Registrant and Kyle Armbrester, dated January 9, 2012 |   | 10-Q |   | 001-33689 |   | October 22, 2015 |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.11 |   | Separation Agreement by and between the Registrant and Kristi Matus, dated May 31, 2016 |   | 10-Q |   | 001-33689 |   | July 21, 2016 |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.12 |   | athenahealth, Inc. Executive Incentive Plan, adopted March 29, 2013 |   | 8-K |   | 001-33689 |   | April 4, 2013 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.13        |   | Office Lease Agreement by and between the Registrant and JAMESTOWN Ponce City Market, L.P., dated June 24, 2013 |   | 10-Q |   | 001-33689 |   | July 19, 2013 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.14        |   | Amendment No. 1 to Office Lease Agreement by and between the Registrant and JAMESTOWN Ponce City Market, L.P., dated April 23, 2014 |   | 10-Q |   | 001-33689 |   | July 18, 2014 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.15        |   | Amendment No. 2 to Office Lease Agreement by and between the Registrant and JAMESTOWN Ponce City Market, L.P., dated August 18, 2014 |   | 10-Q |   | 001-33689 |   | October 17, 2014 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.16        |   | Amendment No. 3 to Office Lease Agreement by and between the Registrant and JAMESTOWN Ponce City Market, L.P., dated February 27, 2015 |   | 10-K |   | 001-33689 |   | February 4, 2016 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.17        |   | Amendment No. 4 to Office Lease Agreement by and between the Registrant and JAMESTOWN Ponce City Market, L.P., dated July 27, 2015 |   | 10-K |   | 001-33689 |   | February 4, 2016 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.18        |   | Purchase and Sale Agreement by and between the Registrant and the President and Fellows of Harvard College, dated December 5, 2012 |   | 10-K |   | 001-33689 |   | February 11, 2013 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.19        |   | First Amendment to Purchase and Sale Agreement by and between athenahealth, Inc. and President and Fellows of Harvard College, dated March 12, 2013 |   | 8-K |   | 001-33689 |   | March 18, 2013 |   |
|         |   |   |   |   |   |   |   |   |   |

----

|              |
|--------------|
|              |  |  |  |  |  |  |  |  |  |
| ExhibitNo.   |   | Exhibit Description |   | Incorporated by Reference |   |
| 10.20        |   | Credit Agreement among the Registrant, Bank of America, N.A., as Administrative Agent, Swing Line Lender, and Letter of Credit Issuer, the other lenders party thereto, and Merrill Lynch, Pierce, Fenner & Smith Incorporated and TD Securities (USA) LLC as Joint Lead Arrangers and Joint Book Managers, dated May 10, 2013, and exhibits and schedules thereunder |   | 10-Q |   | 001-33689 |   | July 19, 2013 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.21        |   | First Amendment to Credit Agreement among the Registrant, Bank of America, N.A., as Administrative Agent, dated December 18, 2014 |   | 8-K |   | 001-33689 |   | December 24, 2014 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.22        |   | Amended and Restated Credit Agreement by and between the Registrant and Bank of America, N.A. as Administrative Agent, Swing Line Lender, and Letter of Credit Issuer; the other lenders party thereto from time to time; and Merrill Lynch, Pierce, Fenner & Smith Incorporated, TD Securities (USA) LLC, and U.S. Bank National Association as Joint Lead Arrangers and Joint Book Managers, dated May 5, 2015 |   | 10-Q |   | 001-33689 |   | July 23, 2015 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.23        |   | Seaholm Triple Net Lease, effective as of January 31, 2014 |   | 10-Q |   | 001-33689 |   | April 18, 2014 |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.24        |   | First Amendment to Lease by and between the Registrant and Seaholm L/R, LLC, dated May 12, 2015 |   | 10-Q |   | 001-33689 |   | July 23, 2015 |   |
|         |   |   |   |   |   |   |   |   |   |
| #10.25*      |   | Services Agreement by and between the Registrant and Access Healthcare Services USA, LLC, dated July 31, 2013 |   |   |   |   |   |   |   |
|         |   |   |   |   |   |   |   |   |   |
| 10.26        |   | Construction Management Agreement by and between Athena Arsenal, LLC, a subsidiary of the Registrant, and C.E. Floyd Company, Inc., dated December 5, 2016 |   | 10-K |   | 001-33689 |   | February 2, 2017 |   |
|         |   |   |   |   |   |   |   |   |   |
| †10.27 |   | Director Compensation Plan of the Registrant, effective as of January 1, 2017 |   | 10-K |   | 001-33689 |   | February 2, 2017 |   |
|         |   |   |   |   |   |   |   |   |   |
| 21.1         |   | Subsidiaries of the Registrant |   | 10-K |   | 001-33689 |   | February 2, 2017 |   |
|         |   |   |   |   |   |   |   |   |
| 23.1         |   | Consent of Independent Registered Public Accounting Firm |   | 10-K |   | 001-33689 |   | February 2, 2017 |   |
|         |   |   |   |   |   |   |   |   |
| 31.1*        |   | Rule 13a-14(a) or 15d-14 Certification of Chief Executive Officer |   |   |   |   |   |   |   |
|         |   |   |   |   |   |   |   |   |
| 31.2*        |   | Rule 13a-14(a) or 15d-14 Certification of Chief Financial Officer |   |   |   |   |   |   |   |
|         |   |   |   |   |   |   |   |   |
| 32.1         |   | Certifications of Chief Executive Officer and Chief Financial Officer pursuant to Exchange Act rules 13a-14(b) or 15d-14(b) and 18 U.S.C. Section 1350 |   | 10-K |   | 001-33689 |   | February 2, 2017 |   |
|         |   |   |   |   |   |   |   |   |   |
| 101          |   | XBRL (eXtensible Business Reporting Language). The following materials from athenahealth, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2016, formatted in XBRL: (i) the Consolidated Balance Sheets, (ii) the Consolidated Statements of Income, (iii) the Consolidated Statements of Comprehensive Income, (iv) the Consolidated Statements of Stockholders’ Equity, (v) the Consolidated Statements of Cash Flows, and (vi) notes to consolidated financial statements. |   |   |   |   |   |   |   |

|         |
|---------|
|         |  |
| † | Indicates a management contract or any compensatory plan, contract, or arrangement. |

|   |
|---|
|   |  |
| * | Furnished or filed herewith. |

|   |
|---|
|   |  |
| # | Application has been made to the Securities and Exchange Commission for confidential treatment of certain provisions. Omitted material for which confidential treatment has been requested has been filed separately with the Securities and Exchange Commission. |