Exhibit 10.1

ATHENAHEALTH, INC.
DIRECTOR COMPENSATION PLAN
(Effective July 1, 2011)

     The athenahealth, Inc. (the “Company”) Director Compensation Plan (the “Plan”) applies to “non-employee” directors. Non-employee directors shall receive the following compensation for service on the Board of Directors:

Cash Compensation

Meeting Day Fees (1)		Meeting Fee
In Person — Board Meeting		$	3,000
In Person — Committee Meeting		$	3,000
By Phone — Board Meeting and Board Calls		$	1,000
By Phone — Committee Meeting		$	1,000

Retainers (2)		Annual Retainer
Lead Director		$	10,000
Audit Committee Chair		$	20,000
Compensation Committee Chair		$	10,000
Litigation Committee Chair		$	10,000
Nominating and Corporate Governance Committee Chair		$	10,000

Equity Compensation

Annual Grant

Annual equity grants shall be the equivalent in value to $150,000/year. The equity amount will be determined by dividing $150,000 by the average stock price of the Company during the last 20 trading sessions preceding and including the Annual Meeting date to arrive at a restricted stock unit equivalent. Restricted stock units and/or stock options (or any combination of stock options and restricted stock units at a 2:1 ratio) shall be granted with a vesting start date of the first trading day of July of each year, vesting in one year from the vesting start date. Grants for new directors will be pro-rated for partial year service and granted on the first business day of the month following the later of the initial date of service or the date on which such grant is approved. The number of stock options and restricted stock units will be reviewed annually by the Nominating and Corporate Governance Committee and are subject to change. Directors with equity vesting from equity grants granted prior to the effective date of this Director Compensation Plan will not receive new annual grants until all prior equity grants are fully vested unless an exception is made by the Nominating and Corporate Governance Committee.

In addition to the cash and equity compensation described above, the Company reimburses each member of the Board of Directors for reasonable travel and other expenses in connection with attending meetings of the Board of Directors or committees thereof.

This Plan is prospective from the effective date and will not affect any compensation paid or granted before that date. This Plan may be amended from time to time by vote of the Board of Directors. This Plan does not affect the obligations of the Company to indemnify directors as set forth in relevant sections of the Company’s certificate of incorporation, by-laws or indemnification agreements. Questions or issues concerning the application and administration of this Plan will be addressed by the Nominating and Corporate Governance Committee.