Separation Agreement by and between the Registrant and Jonathan Bush dated September 5, 2018

Dear Jonathan,

This letter agreement (the “Agreement”) sets forth the severance payments and benefits to be provided to you in connection with your separation of employment from athenahealth, Inc. and its affiliates (together, the “Company”) on June 6, 2018 (the “Separation Date”).

You acknowledge that as of the Separation Date you have resigned from your position as Chief Executive Officer and President of the Company and have resigned from all offices and directorships held in the Company or its subsidiaries.

1.Accrued Pay and Benefits. You acknowledge and agree that you have received pay for all work you performed for the Company through the Separation Date, as well as pay, at your final base rate of pay, for any vacation days you had earned but not used as of the Separation Date as reflected on the books of the Company, determined in accordance with Company policy. You shall be also be entitled to receive any vested benefits to which you are entitled under the employee benefit plans of the Company, payable pursuant to the terms and conditions of such benefit plans. You acknowledge and agree that the payments described in this Section 1 are in complete satisfaction of any and all compensation due to you from the Company, whether for services provided to the Company or otherwise, through the Separation Date and that, except as expressly provided under this Agreement, no further compensation is owed or will be paid to you.

2.Severance Payments and Benefits. Subject to your execution, delivery and non-revocation of this Agreement during the period set forth in Section 24, and your continued compliance with the terms of this Agreement, including, without limitation, the covenants in Sections 11, 14 and 15 below, the Company will provide you with the following payments and benefits:

3.Equity Incentive Awards. You acknowledge that any unvested equity incentive awards granted to you pursuant to the Company’s 2007 Stock Option and Incentive Plan, as amended and restated as of April 23, 2013 (the “Plan”), were forfeited as of the Separation Date and that, as of the date hereof you hold the vested non-qualified stock options set forth on Exhibit A (the “Options”). You acknowledge and agree that you do not hold any other awards under the Plan. You may exercise the Options within three (3) months following the Separation Date in accordance with the terms of the applicable award agreements governing the Options. Pursuant to Section 5(c)(iv)(C) of the Plan, you are permitted to use the broker directed exercise method to exercise your Options. You and the Company acknowledge that although you may exercise the Options pursuant to Section 5(c)(iv)(C) of the Plan, while you are in possession of material non-public information concerning the Company, payment of the exercise price may not be effected. Accordingly, a transfer of the shares subject to the exercise of the Options will not occur until payment of the exercise price is received by the Company, in accordance with the terms of Section 5 of the Plan. If you elect to exercise all or a portion of the Options pursuant to Section 5(c)(iv)(C) of the Plan, then pursuant to Section 20(b) of the Plan, which permits the Company to impose any timing or other restrictions with respect to the exercise of any award, your payment of the exercise price and the transfer to you of the shares subject to the exercise of the Options shall occur no later than the earlier of (i) the date on which you are no longer in possession of material non-public information, or (ii) the occurrence of a Change in Control (as defined in the Company’s Change in Control Severance Plan for Certain U.S. Officers and Executives effective October 23, 2017 (the “CIC Severance Plan”)). The Company agrees to notify you at such time, based on the Company’s actual knowledge, that it believes you are no longer in possession of material non-public information concerning the Company. Notwithstanding the foregoing, you acknowledge that (i) you have received no information about the Company that would constitute material non-public information since the Separation Date from any party whether or not affiliated with the Company and (ii) the Company is not responsible for your determination of whether you are in possession of material non-public information.

4.Expenses. In signing this Agreement, you acknowledge and agree that you have submitted your final expense reimbursement statement reflecting all business expenses you incurred through the Separation Date for which you seek reimbursement, and, in accordance with Company policy, reasonable substantiation and documentation for the same. The Company will, promptly, but in any event no later than thirty (30) days following the Effective Date, reimburse you for your authorized and documented expenses pursuant to its regular business practices.

5.Incentive. You shall make yourself available to participate in a strategic review of the Company, if and to the extent reasonably requested by the Company. Such participation shall occur during normal business hours or at other mutually convenient times and places, taking into account any employment restraints that you may have, and shall not extend beyond nine (9) months following the Separation Date. In exchange for making yourself available and such potential participation, if, within nine (9) months following the Separation Date (i) a Change in Control (as defined in the CIC Severance Plan) is consummated or (ii) a definitive transaction agreement is entered into by the Company, pursuant to which, if the transaction(s) contemplated thereby were to be consummated, a Change in Control would occur, you shall be entitled to a lump sum payment equal to four million eight hundred and thirty thousand dollars ($4,830,000), payable within thirty (30) days following the consummation of the Change in Control.

6.Additional Payment. You shall be eligible to receive a lump sum cash payment of $2,000,000 within thirty (30) days following January 6, 2020, subject to your continued compliance with all of your obligations under this Agreement, including without limitation Sections 11, 14 and 15, through such date.

7.Sole Payments and Benefits. You acknowledge and agree that the termination payments and benefits set forth in Section 2 are provided to you pursuant to the Company’s Severance Plan for U.S. Officers and Executives effective October 23, 2017 (the “Severance Plan”) and are subject to all terms, conditions, restrictions and limitations of the Severance Plan. The obligation of the Company to make the payments or provide the benefits set forth in Sections 2, 5 and 6 and your right to retain the same, are expressly conditioned upon your continued full performance of your obligations under this Agreement and the accuracy of the representations made by you herein. For the avoidance of doubt, nothing in this Agreement limits any recourse available to the Company under the Severance Plan. You acknowledge and agree that the payments and benefits set forth in Sections 1, 2, 5 and 6 shall be the sole and exclusive payments and benefits to which you shall be entitled in respect of your termination of employment with the Company.

8.Status of Employee Benefits. Except for any right you may have to continue your participation and that of your eligible dependents in the Company’s group medical, dental, and vision plans under the federal law known as “COBRA,” your participation in all employee benefit plans of the Company has ended as of the Separation Date, in accordance with the terms of those plans. You will receive information about your COBRA continuation rights under separate cover.

9.Waiver of Future Employment. In consideration of the terms of this Agreement, you have agreed to and do waive any claims you may have for employment by the Company and have agreed not to seek such employment or reemployment by the Company or, its subsidiaries and affiliates in the future.

10.Release of Claims.

11.Confidentiality, Non-Competition, Non-Solicitation, and Non-Disparagement. You acknowledge that you are and shall remain subject to Article VI of the Severance Plan and you agree to abide by the terms thereof; provided that the noncompetition period set forth in Section 6.02 of the Severance Plan and the nonsolicitation period set forth in Section 6.03 of the Severance Plan shall continue for eighteen (18) months following the Separation Date. You also represent and warrant that you have at all times been in compliance with the provisions of Sections 6.01 (Confidential Information), 6.02 (Noncompetition), 6.03 (Nonsolicitation), and 6.04 (Nondisparagement) of the Severance Plan. You acknowledge that you are and shall remain subject to Section 8(c) of your employment agreement with the Company dated as of November 1, 1999 (as amended as of February 26, 2002) (the “Employment Agreement”).

12.Clawback. In the event you breach any of the covenants described in Section 11 of this Agreement, in addition to any other remedies provided in the Employment Agreement, the Severance Plan or in this Agreement, the Company shall have the right cease providing all payments and benefits under this Agreement, and to recover all payments and benefits previously provided to you under this Agreement, including those described in Sections 2, 3, 5 and 6.

13.Protected Activities. You acknowledge that you continue to have the rights described in Section 6.08 of the Severance Plan. Notwithstanding such rights, you agree that under no circumstance will you be authorized to make any disclosures as to which the Company may assert protections from disclosure under the attorney-client privilege or the attorney work product doctrine, without prior written consent of the Company’s General Counsel or another authorized officer designated by the Company. Further, you acknowledge that, during the course of your employment with the Company, you have from time to time been instructed not to disparage certain former employees of the Company, and you represent that you have at all times complied with those instructions, and you agree that you will continue to abide by those

instructions. You further agree that you will indemnify and hold the Company and its affiliates harmless from any claims against or damages caused to the Company by any violation of those instructions by you.

14.Return of Company Documents and Other Property. In signing this Agreement, you represent and warrant that you have returned to the Company any and all documents, materials and information (in any form) related to the business of the Company, and all keys, access cards, credit cards, computer hardware and software, telephones and all other property of the Company in your possession or control. Further, you represent and warrant that you have not retained any copy or derivation of any documents, materials or information of the Company. You further represent and warrant that you have not, since June 10^th, 2018, attempted to access or use any computer, network or system of the Company, including without limitation the electronic mail system, and you agree that you will not do so in the future. Further, you represent that you have disclosed to the Company all passwords necessary, desirable, or helpful to obtain access to any information which you have password-protected on any computer equipment, network or system of the Company.

15.Cooperation. You agree to reasonably cooperate with, assist and advise the Company hereafter with respect to all matters arising during or relating to your employment, including but not limited to any investigation which may be performed by the Company or any Government Agency or any litigation or regulatory proceeding in which the Company may become involved. Such assistance shall include you making yourself reasonably available for interviews by the Company or its counsel, depositions, and/or court appearances at the Company’s reasonable request. The Company shall attempt to schedule such assistance at mutually convenient times and places, taking into account any employment constraints that you may have. The Company shall reimburse you for all reasonable expenses, such as travel, lodging and meal expenses, incurred by you at the Company’s request, consistent with the Company’s generally applicable policies for employee expenses. To the maximum extent permitted by law, you agree that you will notify the Company’s General Counsel if you are contacted by any person contemplating or maintaining any claim or legal action against the Company, or by any agent or attorney of such person, within three business days of such contact. Your obligations to provide assistance and advice to the Company as required in this Section 15 shall not limit or interfere with your rights under Section 6.08 of the Severance Plan.

16.Withholding. All payments made by the Company under this Agreement shall be reduced by any tax or other amounts required to be withheld by the Company under applicable law and all other lawful deductions authorized by you.

17.Miscellaneous. This Agreement constitutes the entire agreement between you and the Company with regard to the subject matter hereof and supersedes and terminates the Employment Agreement, except to the extent any provisions of the Employment Agreement survive such termination, including, without limitation, Section 8(c) of your Employment Agreement. In the event that any one or more of the provisions of this Agreement are held to be invalid, illegal or unenforceable, the validity, legality and enforceability of the remainder of the Agreement shall not in any way be affected or impaired thereby. No waiver by either party of any breach by the other party of any condition or provision of this Agreement to be performed by such other party shall be deemed a waiver of any other provision or condition at the time or at any prior or subsequent time. This Agreement may not be modified or amended, and no breach shall be deemed to be waived, unless agreed to in writing by you and the General Counsel of the Company or her expressly authorized designee. You agree that any modifications, material or otherwise, made to this Agreement, do not restart or affect in any manner the original consideration period of twenty-one (21) days provided in Section 24 below.

18.Notices. All notices given hereunder shall be given in writing, shall specifically refer to this Agreement and shall be personally delivered or sent by telecopy, facsimile or other electronic transmission or by registered or certified mail, return receipt requested, at the address set forth below or at such other address as may hereafter be designated by notice given in compliance with the terms hereof:

If to the Company:    athenahealth, Inc.

311 Arsenal Street

Watertown, MA 02472

Attn: Jessica Collins, General Counsel

19.Successors and Assigns. This Agreement is intended to bind and inure to the benefit of and be enforceable by you, the Company and your and the Company’s respective heirs, successors and assigns, except that you may not assign your rights or delegate your obligations hereunder without the prior written consent of the Company.

20.Section 409A. The intent of the parties is that payments and benefits provided under this Agreement comply with or be exempt from Section 409A of the Internal Revenue Code of 1986, as amended (“Section 409A”) and, accordingly, to the maximum extent permitted, this Agreement shall be interpreted to be in compliance therewith or exempt therefrom, as applicable. A termination of employment shall not be deemed to have occurred for purposes of this Agreement providing for the payment of any amounts or benefits that are considered nonqualified deferred compensation under Section 409A upon or following a termination of employment, unless such termination is also a “separation from service” within the meaning of Section 409A and the payment thereof prior to a “separation from service” would violate Section 409A. Any payment hereunder constituting “nonqualified deferred compensation” within the meaning of Section 409A will be paid on the day that is six months plus one day after the Separation Date, after applying the exemption for short-term deferrals of compensation in accordance with Section 409A. All expenses or other reimbursements as provided herein shall be payable in accordance with the Company’s policies in effect from time to time, but in any event any reimbursements that are non-qualified deferred compensation subject to Section 409A of the Code shall be made on or prior to the last day of the taxable year following the taxable year in which such expenses were incurred by you. No such reimbursement or expenses eligible for reimbursement in any taxable year shall in any way affect the expenses eligible for reimbursement in any other taxable year and the right to reimbursement or in-kind benefits shall not be subject to liquidation or exchanged for another benefit. For purposes of Section 409A, your right to receive any installment payments pursuant to this Agreement shall be treated as a right to receive a series of separate and distinct payments. Whenever a payment under this Agreement specifies a payment period with reference to a number of days (e.g., “payment shall be made within thirty days following the date of termination”), the actual date of payment within the specified period shall be within the sole discretion of the Company. Nothing contained in this Agreement shall constitute any representation or warranty by the Company regarding compliance with Section 409A.

21.Nonadmission of Wrongdoing. The parties agree that neither this Agreement nor the furnishing of the consideration for this Agreement shall be deemed or construed at any time for any purpose as an admission by the Company or of you of wrongdoing or evidence of any liability or unlawful conduct of any kind.

22.Governing Law; Waiver of Jury Trial. This Agreement shall be subject to, and governed by, the laws of the Commonwealth of Massachusetts applicable to contracts made and to be performed therein, without regard to conflict of laws principles thereof.

24.Knowing and Voluntary Time to Consider and Revoke. You acknowledge that pursuant to Section 10 of this Agreement, you are waiving and releasing any rights you may have under ADEA, and your waiver and release of such rights is knowing and voluntary. You acknowledge that the consideration given for the ADEA waiver and release under Section 10 is in addition to anything of value to which you were already entitled. You further acknowledge that you are advised by this writing that:

(a)you should consult with an attorney prior to executing this Agreement and have had a sufficient opportunity to do so;

(b)you have been provided twenty-one (21) days within which to consider this Agreement;

(c)you have seven (7) days following your execution of this Agreement to revoke it, but only by providing written notice of such revocation to the Company in accordance with the “Notice” provision in Section 18 of this Agreement;

(d)this Agreement shall not become effective and enforceable until the eighth (8th) day following your execution of this Agreement without revocation (i.e. until the Effective Date);

(e)if you revoke this Agreement as provided in Section 24(c) hereof, then this Agreement shall not take effect; and

(f)the twenty-one (21) day period set forth above shall run from the date you receive this Agreement.

25.Counterparts. This Agreement may be executed in counterparts, each of which shall be deemed an original but all of which together shall constitute one and the same instrument.

Please acknowledge your acceptance of the terms of this letter agreement by signing and dating this letter agreement as indicated below.

Accepted and agreed:

Jonathan Bush