<PAGE>

                                                                   EXHIBIT 10.25


          NEITHER THESE WARRANTS NOR THE SHARES UNDERLYING THESE WARRANTS HAVE
          BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 ("1933 ACT") 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 IF NECESSARY, 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 AMENDED AND RESTATED SHAREHOLDERS' AGREEMENT DATED AS OF APRIL
          13, 1999 (THE "SHAREHOLDERS' AGREEMENT"), A COPY OF WHICH MAY BE
          OBTAINED FROM INTRALINKS, INC.


468,000 Warrants                                         April 13, 1999

                              WARRANT CERTIFICATE

                               INTRALINKS, INC.

          This warrant certificate ("Warrant Certificate") certifies that for
value received Ernst & Young U.S. LLP ("E&Y") or registered assigns (the
"Holder") is the owner of the number of warrants (the "Warrants") specified
above, each of which entitles the Holder thereof to purchase, at any time after
such warrants vest in accordance with the terms hereof and on or before the
Expiration Date (as hereinafter defined), one fully paid and non-assessable
share of Series D Convertible Preferred Stock, $.01 par value, (the "Series D
Preferred") of IntraLinks, Inc. (the "Company"), with such rights and
preferences as are established in the Company's Certificate of Designations for
Series D Preferred Stock (subject to adjustment as hereinafter provided), for
the Purchase Price (defined in Section 1 below) in lawful money of the United
States of America (subject to adjustment as hereinafter provided).

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

     Each Warrant initially shall entitle the Holder to purchase one share of
Series D Preferred of the Company, and the purchase price payable upon exercise
of the Warrant (the "Purchase Price") shall initially be $10.00 per share of
Series D Preferred, subject to adjustment as hereinafter provided.  The Purchase
Price and number of shares of Series D Preferred issuable upon exercise of this
Warrant are subject to adjustment as provided in Section 5 hereof.  The shares
of Series D Preferred issuable upon exercise of the Warrant (and/or other shares
of stock so issuable by reason of any adjustments pursuant to Section 5) are
sometimes referred to herein as the "Warrant Shares."
<PAGE>

     2.   Exercise; Expiration Date; No Fractional Shares; Reservation of Shares
          ----------------------------------------------------------------------

     2.1. The Warrants are exercisable, at the option of the Holder, in whole or
in part once vested in accordance with the terms hereof 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 the Purchase Price. In the case of exercise of less
   ---------
than the entire Warrant 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 Warrant.
The Warrants shall vest as follows: (x) twelve (12) months from the date hereof
(the "First Anniversary"), a number of Warrants shall vest equal to (1) 312,000,
times (2) the Company's aggregate revenues during the 12-month period ending
March 31, 2000 (the "First Year"), divided by (3) $12,100,000 (up to a maximum
of 312,000 Warrants), provided that if the Company's aggregate revenues for the
First Year are less than $10,000,000 no Warrants shall vest on the First
Anniversary; and (y) twenty four (24) months from the date hereof (the "Second
Anniversary"), an aggregate number of Warrants shall vest equal to (A) minus
(B), where (A) is (1) 468,000, times (2) the Company's aggregate revenues during
the 24-month period ending March 31, 2001, divided by (3) $33,100,000 (up to a
maximum of 468,000 Warrants), provided that if the Company's aggregate revenues
for the twelve (12) months ending March 31, 2001 are less than $18,000,000 no
Warrants shall vest on the Second Anniversary, and (B) is the number of Warrants
that vested on the First Anniversary. If the combined aggregate revenues for the
24-month period from the date hereof are greater than or equal to $33,100,000,
all unvested Warrants will vest on the Second Anniversary. Any warrants which do
not vest on or before the Second Anniversary shall expire at that time.
Notwithstanding the foregoing, in the event of (i) the consummation of an
underwritten public offering of shares of the Company's Common Stock (as defined
herein) resulting in net proceeds to the Company of not less than $25 million at
a per share common stock equivalent price of at least $19.50 or (ii) a change in
control of the Company, any unvested and unexpired warrants shall vest and
become immediately exercisable. As used in the previous sentence, "change of
control" means a merger or consolidation of the Company or the sale of more that
50% of the capital stock or assets of the Company.

     2.2. The term "Expiration Date" shall mean 5:00 p.m. New York time five
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.

     2.3. No fractional shares shall be issued upon exercise or conversion (in
whole or in part) of the Warrants and the number of shares of Series D Preferred
to be issued shall be rounded down to the nearest whole share, and there shall
be no payment to the Holder for any such rounded fractional shares.

     2.4. 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 and conversion of the Series D Preferred to the
common stock of the Company, par value $.01 (the

                                       2
<PAGE>

"Common Stock"), such number of shares of Series D Preferred as shall then be
issuable upon the exercise of all outstanding Warrants and such number of shares
of Common Stock as are issuable upon conversion of the Series D Preferred then
issued or issuable upon exercise of the Warrants. The Company covenants that all
shares of capital stock which shall be issuable upon exercise of the Warrants
and upon conversion of the Series D Preferred shall, upon issuance in accordance
with the terms hereof, be duly and validly issued and fully paid and non-
assessable and free from all taxes, liens, encumbrances and charges with respect
to the issue thereof, and that upon issuance the Company shall use its
commercially reasonable efforts to cause such shares to 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.

     2.5. At such time hereafter as all of the Company's outstanding Series D
Preferred has been converted into shares of the Company's Common Stock in
accordance with the Company's Certificate of Incorporation, as amended and/or
restated and effective immediately prior to any such conversion (the
"Certificate"), then this Warrant shall immediately become exercisable for that
number of shares of the Company's Common Stock equal to the number of shares of
Common Stock which would have been received if this Warrant had been exercised
in full and the Series D Preferred received thereupon had been simultaneously
converted into Common Stock immediately prior to the last such conversion of
Series D Preferred Stock.  The per share purchase price shall be immediately
adjusted to equal the quotient obtained by dividing (x) the aggregate Purchase
Price of the number of shares of Series D Preferred for which this Warrant was
exercisable immediately prior to such conversion by (y) the number of shares of
Common Stock for which this Warrant is exercisable immediately after such
conversion or redemption.  In the event that this Warrant becomes exercisable
for Common Stock, any adjustments pursuant to Section 5 shall be determined as
if the provisions of Section 5 related to Common Stock and not to Series D
Preferred.

     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.

     4.   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 Warrant
Shares.

                                       3
<PAGE>

     5.   Adjustment of Purchase Price and Number of Shares Deliverable;
          --------------------------------------------------------------
          Reorganizations and Recapitalizations
          -------------------------------------

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

          (a)  In case the Company shall (i) declare a dividend or make a
distribution on its Series D Preferred payable in shares of its capital stock,
(ii) subdivide its outstanding shares of Series D Preferred through stock split
or otherwise, (iii) combine its outstanding shares of Series D Preferred into a
smaller number of shares of Series D Preferred, or (iv) issue by
reclassification of its Series D Preferred (including any 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 the Warrants 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 or
it would have owned or have been entitled to receive after the happening of any
of the events described above, had such Warrants been exercised immediately
prior to the happening of such event or any record date with respect thereto.
Any adjustment made pursuant to this paragraph (a) shall become effective
retroactively as of the record date of such event.

          (b)  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 Series
D Preferred 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 the Warrants 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 Warrant 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 Section 5 with respect to rights and
interest thereafter of the Holder of the Warrants to the end that the provisions
of this Section 5 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 5.1(b) shall similarly
apply to successive reorganizations, reclassifications, consolidations, mergers,
sales, transfers or other dispositions.

          (c)  Whenever the number of Warrant Shares purchasable upon the
exercise of the Warrants is adjusted, as provided in this Section 5.1, 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 the Warrants immediately prior to such
adjustment, and of

                                       4
<PAGE>

which the denominator shall be the number of Warrant Shares so purchasable
immediately thereafter.

     5.2. Whenever the number of Warrant Shares purchasable upon the exercise of
the 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 the Chief Financial Officer or Secretary 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, a brief statement of the facts requiring such adjustment and the
computation by which such adjustment was made.

     5.3. In the event that at any time prior to the expiration of the Warrants
and prior to their exercise:

          (a)  the Company shall offer for subscription to the holders of the
Series D Preferred any additional shares of stock of any class or any other
securities convertible into Series D Preferred or any rights to subscribe
thereto; or

          (b)  the Company shall declare any stock split, stock dividend,
subdivision, combination, or similar distribution with respect to the Series D
Preferred, regardless of the effect of any such event on the outstanding number
of shares of Series D Preferred; or

          (c)  the Company shall declare a dividend with respect to the Series D
Preferred, other than a dividend payable in shares of the Company's own
Series D Preferred or Common Stock; or

          (d)  there shall be a voluntary or involuntary dissolution,
liquidation, or winding up of the Company (other than in connection with a
consolidation, merger, or sale of all or substantially all of its property,
assets and business as an entity);

          (e)  there shall be any capital change in the Company as set forth in
Section 5.1(b);

(each such event hereinafter being referred to as a "Notification Event"), the
Company shall cause to be mailed to the Holder, not less than 10 days prior to
the record date, if any, in connection with such Notification Event (provided,
however, that if there is no record date, or if 10 days prior notice is
impracticable, as soon as practicable) written notice specifying the nature of
such event and the effective date of, or the date on which the books of the
Company shall close or a record shall be taken with respect to, such event.
Such notice shall also set forth facts indicating the effect of such action, if
any (to the extent such effect may be known at the date of such notice), on the
Purchase Price and the kind and amount of the shares of stock or other
securities or property deliverable upon exercise of the Warrant.

                                       5
<PAGE>

     6.   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.

     7.   Registration Rights
          -------------------

     The Warrants and the Warrant Shares shall have the registration rights set
forth in the Amended and Restated Registration Rights Agreement of even date
herewith by and among the Company, the Holder and the other securityholders of
the Company named therein.

     8.   Governing Law
          -------------

     This Warrant Certificate shall be governed by and construed in accordance
with the laws of the State of New York, without regard to the conflict of law
principles thereof.

                                       6
<PAGE>

          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 13th day of April, 1999.


                              INTRALINKS, INC.



                              By: /s/
                                  ------------------------------
                                  Name:
                                  Title:



Attest:

/s/
------------------------------
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:

                              __________________________________

                              __________________________________

                              __________________________________