<PAGE>

                                                                   EXHIBIT 10.28

                                     WARRANT
                       TO PURCHASE SHARES OF COMMON STOCK
                                       OF
                               ATHENAHEALTH, INC.
                             A DELAWARE CORPORATION

THIS WARRANT HAS BEEN, AND THE SHARES OF COMMON STOCK WHICH MAY BE PURCHASED
PURSUANT TO THE EXERCISE OF THIS WARRANT (THE "WARRANT SHARES") WILL BE,
ACQUIRED SOLELY FOR INVESTMENT AND NOT WITH A VIEW TO, OR FOR RESALE IN
CONNECTION WITH, ANY DISTRIBUTION THEREOF. NEITHER THIS WARRANT NOR THE WARRANT
SHARES (TOGETHER, THE "SECURITIES") HAVE BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933, AS AMENDED (THE "SECURITIES ACT"), OR ANY STATE SECURITIES LAWS.
THE SECURITIES MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED, HYPOTHECATED OR
OTHERWISE TRANSFERRED IN THE ABSENCE OF SUCH REGISTRATION OR AN OPINION OF
COUNSEL SATISFACTORY TO THE COMPANY AND ITS COUNSEL THAT SUCH DISPOSITION IS
EXEMPT FROM THE REGISTRATION AND PROSPECTUS DELIVERY REQUIREMENTS OF THE
SECURITIES ACT AND OF ANY APPLICABLE STATE SECURITIES LAWS.

WARRANT NO.: Pentech-1                           ISSUANCE DATE: NOVEMBER 1, 2002

NO. OF SHARES: 75,000                            VOID AFTER: OCTOBER 31, 2012

THIS CERTIFIES THAT, for value received, Pentech Financial Services, Inc. (the
"Holder") is entitled to subscribe for and purchase from athenahealth, Inc., a
Delaware corporation (the "Company"), 75,000 fully paid and nonassessable shares
(as adjusted pursuant to Section 2 hereof) (the "Warrant Shares") of Common
Stock of the Company ("Common Stock") at a purchase price of $0.62 per share,
(as adjusted pursuant to Section 2 hereof) (the "Exercise Price"), upon the
terms and subject to the conditions hereinafter set forth:

1. EXERCISE RIGHTS.

     (a) Cash Exercise. The purchase rights represented by this Warrant may be
exercised by the Holder at any time and from time to time during the term
hereof, in whole or in part, by delivery to the principal offices of the Company
of this Warrant and a completed and duly executed Notice of Cash Exercise, in
the form attached as Exhibit "A" hereto, accompanied by payment to the Company
of an amount equal to the Exercise Price then in effect multiplied by the number
of Warrant Shares to be purchased by the Holder in connection with such cash
exercise of this Warrant, which amount may be paid, at the election of the
Holder, by wire transfer or delivery of a certified check payable to the order
of the Company.

     (b) Net Issue Exercise.

          (i) In lieu of exercising the purchase rights represented by this
Warrant on a cash basis pursuant to Section 1(a) hereof, the Holder may elect to
exercise such rights represented by this Warrant at any time and from time to
time during the term hereof, in whole or in part, on a net-issue basis by
electing to receive the number of Warrant Shares which are equal in value to the
value of this Warrant (or any portion thereof to be canceled in connection with
such net-issue exercise) at the time of any such net-issue exercise, by delivery
to the principal offices of the Company of this Warrant and a completed and duly
executed Notice of Net-issue Exercise, in the form attached as Exhibit "B"
hereto, properly marked to indicate (A) the number of Warrant Shares to be
delivered to the Holder in connection with such net-issue exercise, (B) the
number of


Common Stock Warrant Agreement          1

<PAGE>

Warrant Shares with respect to which the Warrant is being surrendered in payment
of the aggregate Exercise Price for the Warrant Shares to be delivered to the
Holder in connection with such net-issue exercise, and (C) the number of Warrant
Shares which remain subject to the Warrant after such net-issue exercise, if any
(each as determined in accordance with Section 1(b)(ii) hereof).

          (ii) In the event that the Holder shall elect to exercise the rights
represented by this Warrant in whole or in part on a net-issue basis pursuant to
this Section 1(b) the Company shall issue to the Holder the number of Warrant
Shares determined in accordance with the following formula:

                                    X = Y (A-B)
                                        -------
                                           A

          X = the number of Warrant Shares to be issued to the Holder in
connection with such net-issue exercise.

          Y = the number of Warrant Shares purchasable under this Warrant or the
portion of the Warrant being exercised in connection with such net-issue
exercise.

          A = the Fair Market Value of one share of Common Stock.

          B = the Exercise Price in effect as of the date of such net-issue
exercise (as adjusted pursuant to Section 2 hereof.)

     (c) Fair Market Value. For purposes of this Section 1, the "Fair Market
Value" of the Common Stock shall have the following meanings:

          (i) If the Common Stock is not listed for trading on a national
securities exchange or admitted for trading on a national market system,
then the Fair Market Value of the Common Stock shall be deemed to be the fair
market value of Common Stock as determined in good faith from time to time by
the Board of Directors of the Company (the "Board of Directors"), and receipt
and acknowledgement of this Warrant by the Holder shall be deemed to be an
acknowledgment and acceptance of any such determination of the fair market value
of Common Stock by the Board of Directors as the final and binding determination
of such fair market value for purposes of this Warrant.

          (ii) If the Company's Common Stock is listed for trading on a national
securities exchange or admitted for trading on a national market system, or
closing bid and asked prices therefor are published in the Over-the-counter
Summary in the Western Edition of The Wall Street Journal, then the per share
Fair Market Value of the Common Stock shall be deemed to be the average of
closing price quoted on such national securities exchange or such national
market system for the ten (10) trading days prior to the date of determination
of Fair Market Value of Common Stock in accordance herewith, or if not so
listed, the average of the closing bid and asked prices for the Company's Common
Stock quoted on the Over-the-counter Summary, for the ten (10) trading days
prior to the date of determination of Fair Market Value for Common Stock in
accordance herewith.

     (d) Additional Conditions to Exercise of Warrant. Unless there is a
registration statement declared or ordered effective by the Securities and
Exchange Commission (the "Commission") under the Securities Act which includes
the Warrant Shares to be issued upon the exercise of the rights represented by
this Warrant, such rights may not be exercised unless and until:

          (i) the Company shall have received an Investment Representation
Statement in the form attached as Exhibit "C" hereto, certifying that, among
other things, the


Common Stock Warrant Agreement          2

<PAGE>

Warrant Shares to be issued upon the exercise of the rights represented by this
Warrant are being acquired for investment and not with a view to any sale or
distribution thereof; and

          (ii) each certificate evidencing the Warrant Shares to be issued upon
the exercise of the rights represented by this Warrant shall be stamped or
imprinted with a legend substantially in the following form:

          THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN
          REGISTERED UNDER THE SECURITIES ACT OF 1933 (THE "SECURITIES ACT") AND
          ARE "RESTRICTED SECURITIES" AS DEFINED IN RULE 144 PROMULGATED UNDER
          THE SECURITIES ACT, SUCH SECURITIES MAY NOT BE SOLD, OFFERED FOR SALE,
          PLEDGED, HYPOTHECATED OR OTHERWISE TRANSFERRED EXCEPT (I) PURSUANT TO
          A REGISTRATION STATEMENT DECLARED OR ORDERED EFFECTIVE BY THE
          SECURITIES AND EXCHANGE COMMISSION UNDER THE SECURITIES ACT
          COVERING SUCH SECURITIES, OR (II) IN COMPLIANCE WITH RULE 144, OR
          (III) PURSUANT TO AN OPINION OF COUNSEL SATISFACTORY TO THE ISSUER OF
          SUCH SECURITIES THAT SUCH REGISTRATION OR RULE 144 COMPLIANCE IS NOT
          REQUIRED UNDER THE SECURITIES ACT AS TO SUCH SALE, OFFER OF SALE,
          PLEDGE, HYPOTHECATION OR OTHER TRANSFER. THIS CERTIFICATE MUST BE
          SURRENDERED TO THE ISSUER HEREOF OR ITS TRANSFER AGENT AS A CONDITION
          PRECEDENT TO THE TRANSFER OF ANY INTEREST IN THE SECURITIES
          REPRESENTED HEREBY.

     (e) Fractional Shares. Upon the exercise of the rights represented by this
Warrant, the Company shall not be obligated to issue fractional shares of Common
Stock, and in lieu thereof, the Company shall pay to the Holder an amount in
cash equal to the Fair Market Value per share of Common Stock immediately prior
to such exercise multiplied by such fraction (rounded to the nearest cent).

     (f) Record Ownership of Warrant Shares. The Warrant Shares shall be deemed
to have been issued, and the person in whose name any certificate representing
Warrant Shares shall be issuable upon the exercise of the rights represented by
this Warrant (as indicated in the appropriate Notice of Exercise) shall be
deemed to have become the holder of record of (and shall be treated for all
purposes as the record holder of) the Warrant Shares represented thereby,
immediately prior to the close of business on the date or dates upon which the
rights represented by this Warrant are exercised in accordance with the terms
hereof.

     (g) Stock Certificates. In the event of any exercise of the rights
represented by this Warrant, certificates for the Warrant Shares so purchased
pursuant hereto shall be delivered to the Holder within a reasonable time and,
unless this Warrant has been fully exercised or has expired, a new Warrant
representing the Warrant Shares with respect to which this Warrant shall not
have been exercised shall also be issued to the Holder within such time.

     (h) Issue Taxes. The issuance of certificates for shares of Common Stock
upon the exercise of the rights represented by this Warrant shall be made
without charge to the Holder for any issuance tax in respect thereof, provided,
however, that the Company shall not be required to pay any tax which may be
payable in respect of any transfer involved in the issuance and delivery of any
certificate in a name other than that of the Holder of the Warrant.


Common Stock Warrant Agreement          3

<PAGE>

2. ADJUSTMENT RIGHTS.

     (a) Right to Adjustment. The number of Warrant Shares purchasable upon the
exercise of the rights represented by this Warrant, and the Exercise Price
therefor, shall be subject to adjustment from time to time upon the occurrence
of certain events, as follows:

          (i) Reclassifications. In the event of a reclassification of the
Common Stock other than by stock split, subdivision, consolidation or
combination thereof, the Company shall execute a new Warrant, the terms of which
provide that the holder of this Warrant shall have the right to exercise the
rights represented by such new Warrant, and procure upon such exercise and
payment of the same aggregate Exercise Price then in effect, in lieu of the
shares of Common Stock theretofore issuable upon exercise of the rights
represented by this Warrant, the kind and amount of shares of stock, other
securities, money and property receivable upon such reclassification by a holder
of an equivalent number of shares of Common Stock. Such new Warrant shall
provide for adjustments, which are as equivalent as practicable to the
adjustments provided for in this Section 2. The provisions of this Section
2(a)(i) shall apply with equal force and effect to all successive
reclassifications of the Common Stock.

          (ii) Stock Splits, Dividends, Combinations and Consolidations. In the
event of a stock split, stock dividend or subdivision of or in respect of the
outstanding shares of Common Stock, the number of Warrant Shares issuable upon
the exercise of the rights represented by this Warrant immediately prior to such
stock split, stock dividend or subdivision shall be proportionately increased
and the Exercise Price then in effect shall be proportionately decreased,
effective at the close of business on the date of such stock split, stock
dividend or subdivision, as the case may be. In the event of a reverse stock
split, consolidation, combination or other similar event of or in respect of the
outstanding shares of Common Stock, the number of Warrant Shares issuable upon
the exercise of the rights represented by this Warrant immediately prior to such
reverse stock split, consolidation, combination or other similar event shall be
proportionately decreased and the Exercise Price shall be proportionately
increased, effective at the close of business on the date of such reverse stock
split, consolidation, combination or other similar event, as the case may be.

          (iii) Mergers and Consolidations: Sales of Assets or Stock. In the
event of (1) a merger or consolidation of the Company with or into another
corporation, limited liability company, general or limited partnership, joint
venture, association or other legal entity (other than a merger or consolidation
pursuant to which the Company is the surviving corporation and the shareholders
of the Company immediately preceding such merger or consolidation continue to
own at least fifty percent (50%) of the capital stock of the Company entitled to
vote following the closing of such merger or consolidation and which does not
result in any reclassification of the Warrant Shares issuable upon the exercise
of the rights represented by this Warrant), or (2) the sale of all or
substantially all of the assets or capital stock of the Company, the Company, or
any successor corporation or other legal entity, as the case may be, shall
execute a new Warrant, the terms of which provide that the holder of this
Warrant shall have the right to exercise the rights represented by such new
Warrant, and procure upon such exercise and payment of the same aggregate
Exercise Price then in effect, in lieu of the shares of Common Stock theretofore
issuable upon exercise of the rights represented by this Warrant, the kind and
amount of shares of stock, other securities, money and property receivable upon
such merger, consolidation or sale of assets or capital stock by a holder of an
equivalent number of shares of Common Stock. Such new Warrant shall provide for
adjustments, which are as equivalent as practicable to the adjustments provided
for in this Section 2. The provisions of this Section 2(a)(iii) shall apply with
equal force and effect to all successive mergers, consolidations and sales of
assets and capital stock of the Common Stock.

     (b) Adjustment Notices. Upon any adjustment of the Exercise Price, and any
increase or decrease in the number of Warrant Shares subject to this Warrant, in
accordance with this Section 2, the Company, within sixty (60) days thereafter,
shall give written notice thereof to the Holder at the address of such Holder as
shown on the books of the Company, which notice shall state the Exercise Price
as adjusted and, if applicable, the increased or decreased number of


Common Stock Warrant Agreement         4

<PAGE>

Warrant Shares subject to this Warrant, setting forth in reasonable detail the
method of calculation of each such adjustment.

3. TRANSFER OF WARRANT.

     (a) Requirements for Transfer. This Warrant and the rights represented
hereby are not transferable, except in accordance with the conditions set forth
in this Section 3. In order to effect any transfer of all or a portion of this
Warrant or the Warrant Shares, the Holder hereof shall deliver to the Company a
completed and duly executed Notice of Transfer, in the form attached as Exhibit
"D" hereto.

     (b) Additional Conditions to Transfer of Warrant. Unless there is a
registration statement declared or ordered effective by the commission under the
Securities Act which includes this Warrant, the Warrant may not be transferred
unless and until:

          (i) the Company shall have received from the transferee of the Warrant
a fully executed Investment Representation Statement, in the form attached as
Exhibit "E" hereto, certifying that, among other things, this Warrant is being
acquired for investment and not with a view to any sale or distribution thereof,
and

          (ii) the Company shall have received a written notice from the Holder
which describes the manner and circumstances of the proposed transfer
accompanied by a written opinion of Holder's legal counsel, in form and
substance reasonably satisfactory to the Company, stating that such transfer is
exempt from the registration and prospectus delivery requirements of the
Securities Act and all applicable state securities laws.

4. REPRESENTATIONS AND WARRANTIES OF THE COMPANY. The Company hereby represents
and warrants to the Holder as follows:

     (a) This Warrant has been duly authorized and validly executed and
delivered by the Company and constitutes a valid and legally binding obligation
of the Company enforceable against the Company in accordance with its terms.

     (b) The Warrant Shares have been duly and validly authorized and reserved
for issuance by the Company upon the exercise of the rights represented by this
Warrant and, when issued upon the exercise of such rights in accordance with the
terms and conditions hereof, the Warrant Shares will be (A) duly authorized and
validly issued, fully paid and nonassessable shares of Common Stock, (B) free
from all preemptive rights, rights of first refusal or first offer, taxes,
liens, charges or other encumbrances with respect to the issuance thereof by the
Company, and (C) free of any restrictions on the transfer thereof other than
restrictions on transfer provided for herein or under applicable federal and
state securities laws. At all times during the term hereof, the Company shall
have authorized and reserved for issuance a sufficient number of shares of
Common Stock to provide for the exercise of the rights represented by this
Warrant.

     (c) The due execution and delivery of this Warrant are not, and the
issuance of the Warrant Shares upon the exercise of the rights represented by
this Warrant in accordance with the terms hereof will not, conflict with the
Articles of Incorporation or Bylaws of the Company, each as amended to the date
of issuance hereof.

     (d) The Company acknowledges that this Warrant does not constitute security
for the repayment of any lease, loan or other indebtedness due from the Company
to the Holder.

5. REPRESENTATIONS AND WARRANTIES OF THE HOLDER. The Holder hereby represents
and warrants to the Company as follows:


Common Stock Warrant Agreement         5

<PAGE>

     (a) This Warrant and the Warrant Shares are being acquired for such
Holder's own account, for investment and not with a view to, or for resale in
connection with, any distribution or public offering thereof within the meaning
of the Securities Act. Upon the exercise of the rights represented by this
Warrant, the Holder shall, if so requested by the Company, confirm in writing,
in a form reasonably satisfactory to the Company, that the Warrant Shares
issuable upon the exercise of such rights are being acquired for investment and
not with a view toward distribution or resale thereof.

     (b) The Holder understands that the Warrant and the Warrant Shares have not
been registered under the Securities Act by reason of their issuance in a
transaction exempt from the registration and prospectus delivery requirements of
the Securities Act pursuant to Section 4(2) thereof and Regulation D thereunder,
and that such Warrant and the Warrant Shares, as the case may be, must be held
by the Holder indefinitely, and therefore, that the Holder must bear the
economic risk of such investment, unless a subsequent disposition thereof is
registered under the Securities Act or is exempt from such registration
requirements. The Holder further understands that the Warrant Shares have not
been qualified under the California Securities Law of 1968 (the "California
Law") by reason of their issuance in a transaction exempt from the qualification
requirements of the California Law pursuant to Section 25102(f) thereof, which
exemption depends upon, among other things, the bona fide nature of such
Holder's investment intent expressed herein.

     (c) The Holder has such knowledge and experience in investing in companies
similar to the Company in terms of the Company's stage of development and in
financial and business matters that it is capable of evaluating the merits and
risks of the purchase of this Warrant and the Warrant Shares and of protecting
its interests in connection therewith.

     (d) The Holder is able to bear the economic risk of the purchase of the
Warrant Shares pursuant to the terms of this Warrant.

     (e) The Holder has had an opportunity to discuss the Company's business,
management and financial affairs with the Company's management.

     (f) Holder is an "accredited investor" within the meaning of Rule 501 of
Regulation D, as presently in effect.

6. NO SHAREHOLDER RIGHTS. The Holder of this Warrant (and any transferee hereof)
shall not be entitled to vote on matters submitted for the approval or consent
of the shareholders of the Company or to receive dividends declared on or in
respect of shares of Common Stock, or otherwise be deemed to be the holder of
Common Stock or any other capital stock or other securities of the Company
which may at any time be issuable upon the exercise of the rights represented
hereby for any purpose, nor shall anything contained herein be construed to
confer upon the Holder (or any transferee hereof) any of the rights of a
shareholder of the Company or any right to vote for the election of directors or
upon any matter submitted for the approval or consent of the shareholders, or to
give or withhold consent to any corporate action (whether upon any
recapitalization, issuance of stock, reclassification of stock, merger or
consolidation, conveyance, or otherwise) or to receive notice of meetings, or to
receive dividends or subscription rights or otherwise until this Warrant shall
have been exercised and the Warrant Shares issuable upon the exercise of the
rights represented hereby shall have become deliverable as provided herein.

7. REGISTRATION RIGHTS. The Holder shall be entitled to participate in
Piggy-back Registrations as set forth in Section 1.1 of that certain Amended And
Restated Investor Rights Agreement dated as of November 17, 2000, as amended, to
the same extent as the holders of the Company's Registrable Shares, as defined
therein.


Common Stock Warrant Agreement         6

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8. EXPIRATION OF WARRANT. This Warrant shall expire, and the rights represented
hereby may no longer be exercised on the close of business on the tenth
anniversary of the date of issuance hereof.

9. LOCK-UP AGREEMENT. The Holder hereby agrees that, upon request of the
Company or the managing underwriter of a public offering of any securities of
the Company, such Holder shall not sell, make any short sale of, loan, grant any
option for the purchase of, or otherwise dispose of all or any portion of the
Warrant Shares without the prior written consent of the Company or the managing
underwriter, as the case may be, for such period of time (not to exceed one
hundred eighty (180) days from the date upon which the registration statement
relating to such public offering is declared or ordered effective by the
Securities and Exchange Commission) as may be requested by the Company or the
underwriters, as the case may be.

10. MISCELLANEOUS.

     (a) Governing Law. This Warrant is being delivered in the State of
Delaware, and shall be construed and enforced in accordance with and governed by
the laws of such State. The parties expressly stipulate that any litigation
under this Warrant shall be brought in the State or Federal courts of Delaware.
The parties agree to submit to the jurisdiction and venue of such courts.

     (b) Notice Procedures. Any written notice by the Company required hereunder
shall be made by hand delivery or first class mail, postage prepaid, address to
the Holder at the address set forth on the books of the Company.

     (c) Successors and Assigns. The terms of this Warrant shall be binding upon
and shall inure to the benefit of any successors or assigns of the Company and
of the Holder or Holders of this Warrant and the Warrant Shares issued or
issuable upon the exercise of the rights represented by this Warrant.

     (d) Entire Agreement. This Warrant constitutes the full and entire
understanding and agreement between the parties with respect to the subject
matter hereof and supersedes in their entirety any prior or contemporaneous
agreements by and between the Company and the Holder with respect to such
matters.

     (e) Further Assurances: No Impairment. The Company shall not, by amendment
of its Articles of Incorporation or through any other means, directly or
indirectly, avoid or seek to avoid the observance or performance of any of the
terms of this Warrant and shall at all times in good faith assist in the
carrying out of all such terms and in the taking of all such action as may be
necessary or appropriate in order to protect the rights of the holder of this
Warrant against impairment. The Company shall at no time close its transfer
books against the transfer of this Warrant or of any Warrant Shares issued or
issuable upon the exercise of the rights represented by this Warrant in any
manner, which interferes with a timely exercise of such rights.

     (f) Lost Warrant. Upon receipt of evidence reasonably satisfactory to the
Company of the loss, theft, destruction or mutilation of this Warrant and, in
the case of any such loss, theft or destruction, upon delivery of an indemnity
agreement reasonably satisfactory in form and amount to the Company or, in the
case of any such mutilation, upon surrender and cancellation of such Warrant,
the Company at the Holder's expense shall execute and deliver to the Holder, in
lieu thereof, a new Warrant of like date and tenor.

     (g) Amendments. This Warrant and any provision hereof may be amended,
waived or terminated (either generally or in a particular instance,
retroactively or prospectively and for a specified period of time or
indefinitely) only by a written instrument signed by the Company and the Holder,
or, in the event of any partial transfer of the rights represented by this
Warrant, the Holders of rights to purchase more than fifty percent (50%) of the
Warrant Shares issuable upon exercise of


Common Stock Warrant Agreement         7

<PAGE>

the rights represented by this Warrant, and with the same consent the Company
may enter into a supplementary agreement for the purpose of adding any
provisions to or changing in any manner or eliminating any of the provisions of
this Warrant or the Warrants, as the case may be, provided, however, that no
such amendment, waiver, termination or supplemental agreement shall reduce the
aforesaid percentage which is required for consent to any amendment, waiver,
termination or supplemental agreement without the consent of all of the Holders
of the rights represented by this Warrant.

     (h) Headings. The descriptive headings of the paragraphs of this Warrant
are inserted for convenience only and do not constitute a part of this Warrant.

     (i) Survival. All representations and warranties of the Company and the
Holder contained herein shall survive the date of issuance of this Warrant, the
exercise or conversion of this Warrant (or any part hereof) or the termination
or expiration of rights hereunder.

     (j) Severability. The invalidity or unenforceability of any provision of
this Warrant in any jurisdiction shall not affect the validity or enforceability
of such provision in any other jurisdiction, or affect any other provision of
this Warrant, which shall remain in full force and effect.

IN WITNESS WHEREOF, the Company has caused this Warrant to be signed by its duly
authorized officer.

Issued this 1st day of November, 2002.

                                        ATHENAHEALTH, INC.,
                                        A DELAWARE CORPORATION


                                        By: /s/ Carl Byers
                                            ------------------------------------
                                        Name: Carl Byers
                                        Title: CFO

Acknowledged and Accepted:

PENTECH FINANCIAL SERVICES, INC.
A CALIFORNIA CORPORATION


By: /s/ Norman H. Nelson
    ---------------------------------
Name: Norman H. Nelson
Title: President & COO

Date:
      -------------------------------


Common Stock Warrant Agreement         8