Exhibit 10.1

The athenahealth Executive Incentive Plan

I.

Purpose – The purpose of the Executive Incentive Plan (the “Plan”) of
athenahealth, Inc. (the “Company”) is to:

a. attract, retain, and motivate the highest quality executives; b. provide
participants with significant incentive through focus of our resources on our
business strategy by maximizing revenue, managing expenses, and enabling the
Company to produce long-term growth, thereby increasing the Company’s value to
the Company’s shareholders; and c. foster a cooperative teaching and learning
environment that focuses on delivering shareholder value, providing the highest
level of service to our clients, and respecting each other. II.

Overview – The Plan has two parts, one for the Chief Executive Officer (the
“CEO”) and another plan for the heads of the corporate or divisional areas.
These plans are designed to reward the Company’s eligible executives (the
“Participants”) specifically for the performance of the Company’s business
strategy. Individual award amounts are determined by the results of the overall
Company and each Participant’s divisional results. Awards are paid annually for
the CEO Incentive and quarterly for the Corporate/Divisional Incentive.

III.

Plan Period – The Plan will be effective from January 1st, until December 31st,
(the “Plan Period”).

a. For the CEO Incentive Plan payments of awards will be made annually and it is
the intent of the Plan that the payment shall be paid within 73 days of the
close of the Plan Period. b. For the Corporate/Divisional Incentive Plan
payments of awards will be made quarterly and it is the intent of the Plan that
payments for quarters 1, 2 and 3 be paid within 30 days of the close of that
quarter. In the case of the 4th Quarter award, it is the intent of the Plan that
payments shall be paid within 73 days of the close of the Plan Period. IV.

Plan Eligibility – In order to be considered eligible for an award under the
Plan, a Participant must:

a. be an actively employed regular full-time or regular part-time employee in
good standing of the Company or one of its subsidiaries during the Plan Period;

b.

for the CEO Incentive Plan, be the Company’s named Chief Executive Officer; c.
for the Corporate/Divisional Incentive Plan, be a Senior Vice President or
Executive Vice President in charge of a division of the Company or with
Company-wide responsibilities; d. not be a participant in another stand-alone
incentive plan of the Company or any of its subsidiaries; e. not be on written
or oral performance warning; and

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f.

be an actively employed regular full-time or regular part-time employee in good
standing of the Company or one of its subsidiaries as of the date of the award
payout (the “Award Date”). V.

Change of Control – Participants who are terminated as the result of a change in
control of the Company, as determined in the sole and absolute discretion of the
Company’s Board of Directors and, in the case of the Corporate/Divisional
Incentive Plan, the CEO will be eligible for payment of awards for that portion
of the Plan Period pro-rated through the date of termination.

VI.

Death – If a Participant’s employment is terminated by reason of death that
Participant shall cease to be a Participant in the Plan as of the date of death,
but will remain eligible for payment of an award pro rated for time of his or
her participation in the Plan prior to point of death. The award will be paid to
the Participant’s estate or other legally designated beneficiary.

VII.

Disability/Retirement – If a Participant’s employment is terminated by reason of
disability or retirement, he or she shall cease to be a Participant in the Plan
on the effective date of such disability or retirement, but will remain eligible
for payment of an award pro rated for the time of his or her participation in
the Plan prior to point of disability or retirement.

VIII.

New Hires/Transfers In – An employee becomes a Participant upon being hired or
transferred into a Plan-eligible position during the Plan Period and qualifies
for payment of an award as outlined in Section XIII, Individual Awards. The
Participant is eligible for payment of an award pro-rated for their time in the
Plan starting at the point of hire/transfer in to the end of the Quarter in
which the change took place.

IX.

Promotions/Other Changes in Positions (to Ineligible Positions) – A Participant
whose position changes (lateral transfer, demotion, etc.) within the Company to
a position ineligible for participation in the Plan during the Plan Period shall
cease to be a Participant in the Plan on the effective date of such
promotion/change in position, but will remain eligible for payment of an award
pro-rated for the Participant’s time in the Plan prior to the point of the
promotion/change in position.

X.

Promotions/Other Changes in Positions (to Eligible Positions) – A Participant
whose position changes (lateral transfer, demotion, etc.) within the Company to
a position eligible for participation in the Plan during the Plan Period shall
be a Participant in the Plan on the effective date of such promotion/change in
position. That Participant will remain eligible for payment of an award with the
pool funded at his or her current funding target levels.

XI.

Termination – If a Participant voluntarily or involuntarily terminates his or
her employment with the Company prior to the Award Date, he or she shall forfeit
any unpaid awards.

XII.

Funding

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a. Overall Plan Funding – The Plan begins to fund as the Company starts to
attain its threshold Company corporate scorecard targets. The Plan funds fully
upon achievement of the Company’s corporate scorecard targets. The funding of
the Plan may be increased or decreased based on Company performance as
determined by the Compensation Committee of the Company, the Board of Directors,
and the CEO in their absolute discretion. b. CEO Award Pool Funding – The Board
of Directors in their absolute discretion will determine the criteria for the
allocation of the Overall Plan Funding. Performance is based on the level of Net
Income. Finance determines the level of awards based upon Net Income achievement
and will make award recommendations to the Board of Directors, accordingly. c.
Corporate Award Pool Funding – The CEO in his or her absolute discretion will
determine the criteria for the allocation of the Overall Plan Funding.
Performance criteria may vary from year to yearand shall be announced separately
by the CEO. Finance determines the total award pool based upon corporate
scorecard achievement and fundinf targets by job levels and salaries and will
make award recommendations to the CEO, accordingly. Payment – It is the
Company’s intent to pay the accrued Award out fully, without reductions due to
changes in the number of Participants between December 31 and the Award Date.
XIII.

Individual Awards –

a. CEO Award i. The Board of Directors in their absolute discretion will
determine the general criteria that apply to the allocation of the CEO Award.
ii. Participants are subject to maxima for awards as determined by the size of
the Award Pool and/or guidelines allocated to the CEO. 1. The Participant will
have performance targets set in relation to the division in which he or she
works. 2. The Participant’s awards will be based on that Participant’s
contribution to Corporate objectives as well as individual business goals. 3.
Total cash compensation (base salary plus incentive award) is considered and may
affect the final award. iii. Actual awards will depend on the Company’s Net
Income and the performance of the Participant. iv. Final awards are subject to
the approval of the Board of Directors. v. Awards are paid in cash unless
otherwise designated by the Board of Directors. b. Corporate Awards i. The CEO
in his or her absolute discretion will determine the general criteria that apply
to the allocation of individual awards. ii. Participants are subject to maxima
for awards as determined by the size of the Award Pool and/or guidelines
allocated by the CEO.

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1. Each Participant will have individual performance targets set in relation to
the division in which he or she works. 2. Each Participant’s awards will be
based on that Participant’s contribution to Company as well as individual
business goals. 3. Total cash compensation (base salary plus incentive award) is
considered and may affect the final awards. iii. Actual awards will depend on
the Company’s overall performance and the performance of the individual
Participants. iv. Final awards are subject to the approval of the CEO. v. Awards
are paid in cash unless otherwise designated by the CEO. XIV.

Legal Statement

a. Employment and Governing Law – The Plan is subject to the laws of the
Commonwealth of Massachusetts and does not imply any form of continued
employment. b. Amending the Plan – This Plan may be subject to change in part or
in whole without notice at the discretion of the Company’s Board of Directors
and the CEO (the “Plan Administrators”). The Plan Administrators also reserve
the right to terminate the Plan at any time without notice. c. Tax Withholding –
No part of any award shall be required to be delivered until the applicable
Participant (or, if that Participant is deceased, his or her estate or legally
appointed beneficiary) has had the full amount of required tax withholding due
in connection with such award delivery withheld or has made other provisions
satisfactory to the Company for the required tax withholding due in connection
with such award delivery. d. Benefits – The award amounts may not be counted as
part of any pension, retirement, or benefits plan unless specifically stated
within the plan document of that particular pension, retirement, or benefits
plan.

This Plan Document is effective 1/1/10 and supersedes any prior annual incentive
plan document)

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Appendix

2010 SVP Corporate Incentive Plan Targets and Weightings

          Executive

Low

(“Below”

Rating)

Target

(“Meets”

Rating)

High

(“Exceeds”

Rating)

Corporate

Weighting

Divisional

Executives

40% 60% 70% 100%

Notes:

 

●

The above table describes the levels and weightings by the Participant’s
position.

●

Actual awards are a factor of Company funding based on the performance of
Company results against plan (the scorecard); and

●

The Low, Target and High award percentages listed above are applicable to each
Participant and are based upon their performance appraisal rating as determined
by the CEO from the prior Plan Year.

●

For every percentage point over (or under) the weighted Company target, the
Participant’s Incentive target will increase (or in the case of being under
target, decrease) by 2 percentage points for a maximum potential award of 100%
of the eligible earned base salary.