<PAGE>

                                                                   EXHIBIT 10.31

          NEITHER THESE WARRANTS NOR THE SHARES UNDERLYING THESE
          WARRANTS HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF
          1933 OR THE LAWS OF ANY STATE. THEY MAY NOT BE SOLD OR
          OTHERWISE TRANSFERRED UNLESS THEY ARE REGISTERED UNDER SUCH
          ACT AND APPLICABLE STATE SECURITIES LAWS OR AN EXEMPTION
          FROM REGISTRATION IS AVAILABLE. THESE WARRANTS AND THE
          SHARES UNDERLYING THESE WARRANTS ARE ALSO SUBJECT TO
          ADDITIONAL RESTRICTIONS ON TRANSFER SET FORTH IN THE
          PURCHASE AGREEMENT OF EVEN DATE HEREWITH, A COPY OF WHICH
          MAY BE OBTAINED FROM INTRALINKS, INC.

                                                                 40,000 Warrants


                               INTRALINKS, INC.

                              WARRANT CERTIFICATE


          This warrant certificate ("Warrant Certificate") certifies that for
value received, John Sculley or registered assigns (the "Holder") is the owner
of the number of warrants ("Warrants") specified above, each of which entitles
the Holder thereof to purchase, at any time on or before the Expiration Date
(hereinafter defined) one fully paid and non-assessable share of Common Stock,
par value $0.01 per share ("Common Stock"), of IntraLinks, Inc., a Delaware
corporation (the "Company"), at a purchase price of $3.333333 per share of
Common Stock in lawful money of the United States of America in cash or by
certified or cashier's check or a combination of cash and certified or cashier's
check (subject to adjustment as hereinafter provided).

     1.   Warrant; Purchase Price
          -----------------------

          Each Warrant shall entitle the Holder initially to purchase one share
of Common Stock of the Company and the purchase price payable upon exercise of
the Warrants (the "Purchase Price") shall initially be $3.333333 per share of
Common Stock.  The Purchase Price and number of shares of Common Stock issuable
upon exercise of each Warrant are subject to adjustment as provided in Article
6.  The shares of Common Stock issuable upon exercise of the Warrants (and/or
other shares of Common Stock so issuable by reason of any adjustments pursuant
to Article 6) are sometimes referred to herein as the "Warrant Shares."
<PAGE>

     2.   Exercise; Expiration Date
          -------------------------

          2.1.  The Warrants are exercisable, at the option of the Holder, in
whole or in part at any time and from time to time after issuance and on or
before the Expiration Date, upon surrender of this Warrant Certificate to the
Company together with a duly completed Notice of Exercise, in the form attached
hereto as EXHIBIT A, and payment of an amount equal to the Purchase Price times
the number of Warrants to be exercised.  In the case of exercise of less than
all the Warrants represented by this Warrant Certificate, the Company shall
cancel the Warrant Certificate upon the surrender thereof and shall execute and
deliver a new Warrant Certificate for the balance of such Warrants.

          2.2.  The term "Expiration Date" shall mean 5:00 p.m. New York time
FIVE (5) years from the date hereof, or if such day shall in the State of New
York be a holiday or a day on which banks are authorized to close, then 5:00
p.m. New York time the next following day which in the State of New York is not
a holiday or a day on which banks are authorized to close.

     3.   Registration and Transfer on Company Books
          ------------------------------------------

          3.1.  The Company shall maintain books for the registration and
transfer of the Warrants and the registration and transfer of the Warrant
Shares.

          3.2.  Prior to due presentment for registration of transfer of this
Warrant Certificate, or the Warrant Shares, the Company may deem and treat the
registered Holder as the absolute owner thereof.

          3.3.  The Company shall register upon its books any permitted transfer
of a Warrant Certificate, upon surrender of same to the Company with a written
instrument of transfer duly executed by the registered Holder or by a duly
authorized attorney.  Upon any such registration of transfer, new Warrant
Certificate(s) shall be issued to the transferee(s) and the surrendered Warrant
Certificate shall be canceled by the Company.  A Warrant Certificate may also be
exchanged, at the option of the Holder, for new Warrant Certificates of
different denominations representing in the aggregate the number of Warrants
evidenced by the Warrant Certificate surrendered.
<PAGE>

     4.   Reservation of Shares
          ---------------------

          The Company covenants that it will at all times reserve and keep
available out of its authorized capital stock, solely for the purpose of issue
upon exercise of the Warrants, such number of shares as shall then be issuable
upon the exercise of all outstanding Warrants.  The Company covenants that all
shares of capital stock which shall be issuable upon exercise of the Warrants
shall be duly and validly issued and fully paid and non-assessable and free from
all taxes, liens and charges with respect to the issue thereof, and that upon
issuance such shares shall be listed on each national securities exchange, if
any, on which the other shares of such outstanding capital stock of the Company
are then listed.


     5.   Loss or Mutilation
          ------------------

          Upon receipt by the Company of reasonable evidence of the ownership of
and the loss, theft, destruction or mutilation of any Warrant Certificate and,
in the case of loss, theft or destruction, of indemnity reasonably satisfactory
to the Company, or, in the case of mutilation, upon surrender and cancellation
of the mutilated Warrant Certificate, the Company shall execute and deliver in
lieu thereof a new Warrant Certificate representing an equal number of Warrants.


     6.   Adjustment of Purchase Price
          and Number of Shares Deliverable
          --------------------------------

          6.1.  The number of Warrant Shares purchasable upon the exercise of
each Warrant and the Purchase Price with respect to the Warrant Shares shall be
subject to adjustment as follows:

                6.1.1  In case the Company shall (i) declare a dividend or make
     a distribution on its Common Stock payable in shares of its capital stock,
     (ii) subdivide its outstanding shares of Common Stock through stock split
     or otherwise, (iii) combine its outstanding shares of Common Stock into a
     smaller number of shares of Common Stock, or (iv) issue by reclassification
     of its Common Stock (including any such reclassification in connection with
     a consolidation or merger in which the Company is the continuing
     corporation) other securities of the Company, the number and/or nature of
     Warrant Shares purchasable upon exercise of each Warrant immediately prior
     thereto shall be adjusted so that the Holder shall be entitled to receive
     the kind and number of Warrant Shares or other securities of the Company
     which he would have owned or have been entitled to receive after the
     happening of any of the events described above, had such Warrant been
     exercised immediately prior to the happening of such event or any record
     date with respect thereto. An adjustment made pursuant to this paragraph
     (a) shall become effective retroactively as of the record date of such
     event.
<PAGE>

               6.1.2.  In the event of any capital reorganization or any
     reclassification of the capital stock of the Company or in case of the
     consolidation or merger of the Company with another corporation (other than
     a consolidation or merger in which the outstanding shares of the Company's
     Common Stock are not converted into or exchanged for other rights or
     interests), or in the case of any sale, transfer or other disposition to
     another corporation of all or substantially all the properties and assets
     of the Company, the Holder of each Warrant shall thereafter be entitled to
     purchase (and it shall be a condition to the consummation of any such
     reorganization, reclassification, consolidation, merger, sale, transfer or
     other disposition that appropriate provisions shall be made so that such
     Holder shall thereafter be entitled to purchase) the kind and amount of
     shares of stock and other securities and property (including cash) which
     the Holder would have been entitled to receive had such Warrants been
     exercised immediately prior to the effective date of such reorganization,
     reclassification, consolidation, merger, sale, transfer or other
     disposition; and in any such case appropriate adjustments shall be made in
     the application of the provisions of this Article 6 with respect to rights
     and interest thereafter of the Holder of the Warrants to the end that the
     provisions of this Article 6 shall thereafter be applicable, as near as
     reasonably may be, in relation to any shares or other property thereafter
     purchasable upon the exercise of the Warrants. The provisions of this
     Section 6.1(b) shall similarly apply to successive reorganizations,
     reclassifications, consolidations, mergers, sales, transfers or other
     dispositions.

               6.1.3  Whenever the number of Warrant Shares purchasable upon the
     exercise of each Warrant is adjusted, as provided in this Section 6.1, the
     Purchase Price with respect to the Warrant Shares shall be adjusted by
     multiplying such Purchase Price immediately prior to such adjustment by a
     fraction, of which the numerator shall be the number of Warrant Shares
     purchasable upon the exercise of each Warrant immediately prior to such
     adjustment, and of which the denominator shall be the number of Warrant
     Shares so purchasable immediately thereafter.

          6.2.  No adjustment in the number of Warrant Shares purchasable under
the Warrants, or in the Purchase Price with respect to the Warrant Shares, shall
be required unless such adjustment would require an increase or decrease of at
least 1% in the number of Warrant Shares issuable upon the exercise of such
Warrant, or in the Purchase Price thereof; provided, however, that any
adjustments which by reason of this Section 6.2 are not required to be made
shall be carried forward and taken into account in any subsequent adjustment.

          6.3.  Whenever the number of Warrant Shares purchasable upon the
exercise of each Warrant or the Purchase Price of such Warrant Shares is
adjusted, as herein provided, the Company shall mail to the Holder, at the
address of the Holder shown on the books of the Company, a notice of such
adjustment or adjustments, prepared and signed by an officer of the Company,
which sets forth the number of Warrant Shares purchasable upon the exercise of
each Warrant and the Purchase Price of such Warrant Shares after such
adjustment, and a brief statement of the facts requiring such adjustment.
<PAGE>

          6.4.  The form of Warrant Certificate need not be changed because of
any change in the Purchase Price, the number of Warrant Shares issuable upon the
exercise of a Warrant or the number of Warrants outstanding pursuant to this
Section 6, and Warrant Certificates issued before or after such change may state
the same Purchase Price, the same number of Warrants, and the same number of
Warrant Shares issuable upon exercise of Warrants as are stated in the Warrant
Certificates theretofore issued pursuant to this Agreement.  The Company may,
however, at any time, in its sole discretion, make any change in the form of
Warrant Certificate that it may deem appropriate and that does not affect the
substance thereof, and any Warrant Certificates thereafter issued or
countersigned, whether in exchange or substitution for an outstanding Warrant
Certificate or otherwise, may be in the form as so changed.

     7.  Voluntary Adjustment by the Company
         -----------------------------------

         The Company may, at its option, at any time during the term of the
Warrants, reduce the then current Purchase Price to any amount deemed
appropriate by the Board of Directors of the Company and/or extend the date of
the expiration of the Warrants.

     8.   Fractional Shares and Warrants;
          Determination of Market Price Per Share
          ---------------------------------------

          8.1.  Anything contained herein to the contrary notwithstanding, the
Company shall not be required to issue any fraction of a share of Common Stock
in connection with the exercise of Warrants.  Warrants may not be exercised in
such number as would result (except for the provisions of this paragraph) in the
issuance of a fraction of a share of Common Stock unless the Holder is
exercising all Warrants then owned by the Holder.  In such event, the Company
shall, upon the exercise of all of such Warrants, issue to the Holder the
largest aggregate whole number of shares of Common Stock called for thereby upon
receipt of the Purchase Price for all of such Warrants and pay a sum in cash
equal to the remaining fraction of a share of Common Stock, multiplied by its
Market Price Per Share (as determined pursuant to Section 8.2 below) as of the
last business day preceding the date on which the Warrants are presented for
exercise.

          8.2.  As used herein, the "Market Price Per Share" with respect to any
class or series of Common Stock on any date shall mean the closing price per
share of such class or series of Common Stock for the trading day immediately
preceding such date.  The closing price for each such day shall be the last sale
price regular way or, in case no such sale takes place on such day, the average
of the closing bid and asked prices regular way, in either case on the principal
securities exchange on which the shares of such Common Stock of the Company are
listed or admitted to trading, the last sale price, or in case no sale takes
place on such day, the average of the closing bid and asked prices of such
Common Stock on NASDAQ or any comparable system, or if such Common Stock is not
reported on NASDAQ, or a comparable system, the average of the closing bid and
asked prices as furnished by two members of the National Association of
Securities Dealers, Inc. selected from time to time by the Company for that
purpose.  If such bid and asked prices are not available, then "Market Price Per
Share" shall be
<PAGE>

equal to the fair market value of such Common Stock as determined in good faith
by the Board of Directors of the Company.

     9.   Restriction Upon Transfer; Securities Law Matters.
          -------------------------------------------------

THESE WARRANTS MAY NOT BE SOLD, TRANSFERRED OR OTHERWISE DISPOSED OF BY THE
HOLDER, EXCEPT AS SPECIFICALLY PROVIDED IN THE PURCHASE AGREEMENT OF EVEN DATE
HEREWITH BETWEEN THE COMPANY AND THE HOLDER.  THIS NOTE HAS NOT BEEN REGISTERED
UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR STATE SECURITIES LAWS AND MAY
NOT BE SOLD, ASSIGNED OR TRANSFERRED UNLESS SUCH SALE, ASSIGNMENT OR TRANSFER OF
SUCH SHARES IS REGISTERED UNDER THE ACT AND APPLICABLE STATE SECURITIES LAWS OR
UNLESS AN EXEMPTION FROM REGISTRATION IS AVAILABLE.

     10.  Governing Law
          -------------

          This Warrant Certificate shall be governed by and construed in
accordance with the laws of the State of Delaware.

     IN WITNESS WHEREOF, the Company has caused this Warrant Certificate to be
duly executed by its officers thereunto duly authorized and its corporate seal
to be affixed hereon, as of this ____ day of September,, 1997.


                                    INTRALINKS, INC.



[SEAL]                                By: __________________________
                                          Name:
                                          Title:
<PAGE>

                                                            EXHIBIT A



                                 NOTICE OF EXERCISE


          The undersigned hereby irrevocably elects to exercise, pursuant to
Section 2 of the Warrant Certificate accompanying this Notice of Exercise,
_______ Warrants of the total number of Warrants owned by the undersigned
pursuant to the accompanying Warrant Certificate, and herewith makes payment of
the Purchase Price of such shares in full.



                                   Name of Holder


                                   Signature

                                   Address: