<PAGE>

                                                                     EXHIBIT 3.1

                           SECOND AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION

                                       OF

                          MEDCO HEALTH SOLUTIONS, INC.

     Medco Health Solutions, Inc. (the "Corporation"), a corporation organized
and existing under, and by virtue of, the General Corporation Law of the State
of Delaware (the "DGCL"), does hereby certify as follows:

     1.   The Corporation was originally formed as a limited liability company
by the filing of a certificate of formation under the name "Mergerco Delaware
No. 1, L.L.C." with the Secretary of State of the State of Delaware (the
"Secretary of State") on August 26, 1996. The name of the Corporation was
changed to "Merck-Medco Managed Care, L.L.C." pursuant to a merger effective
upon the filing of a certificate of merger with the Secretary of State on
December 27, 1996. The Corporation converted from a limited liability company to
a corporation effective upon the filing of a certificate of conversion with the
Secretary of State on May 21, 2002. In connection with this conversion, a
certificate of incorporation for the Corporation was filed with the Secretary of
State under the name "MedcoHealth Solutions, Inc." on May 21, 2002. The present
name of the Corporation is "Medco Health Solutions, Inc.," as changed pursuant
to a filing of an Amended and Restated Certificate of Incorporation with the
Secretary of State on June 17, 2002.

     2.   This Second Amended and Restated Certificate of Incorporation of the
Corporation was, in accordance with Sections 242 and 245 of the DGCL, (a) duly
proposed by resolutions adopted and declared advisable by the Board of Directors
of the Corporation (the "Board of Directors") acting by written consent pursuant
to Section 141(f) of the DGCL, (b) approved by written consent of the holder of
all of the outstanding shares of capital stock of the Corporation pursuant to
Section 228 of the DGCL and (c) duly executed by an authorized officer of the
Corporation pursuant to Section 103 of the DGCL.

     3.   This Second Amended and Restated Certificate of Incorporation of the
Corporation restates, integrates and further amends the provisions of the
Corporation's Certificate of Incorporation, as heretofore amended, corrected or
supplemented, and, upon filing with the Secretary of State in accordance with
Section 103, shall supersede the Certificate of Incorporation of the
Corporation, as heretofore amended and restated, corrected or supplemented, and
shall, as it may thereafter be amended in accordance with its terms and
applicable law, be the Certificate of Incorporation of the Corporation.

     4.   Pursuant to Section 103(d) of the DGCL, this Second Amended and
Restated Certificate of Incorporation shall become effective upon filing with
the Secretary of State.

     5.   The text of the Certificate of Incorporation of the Corporation is
hereby amended and restated to read in its entirety as follows:

<PAGE>

     FIRST.   The name of the Corporation is Medco Health Solutions, Inc.

     SECOND.  The address of the Corporation's registered office in the State of
Delaware is Corporation Trust Center, 1209 Orange Street in the City of
Wilmington, County of New Castle, Delaware 19801. The name of its registered
agent at such address is The Corporation Trust Company.

     THIRD.   The purpose of the Corporation is to engage in any lawful act or
activity for which corporations may be organized under the DGCL.

     FOURTH.  The total number of shares of all classes of stock which the
Corporation shall have authority to issue is 1,010,000,000, of which
1,000,000,000 shares with the par value of $0.01 per share shall constitute a
class designated as Common Stock, and 10,000,000 shares with the par value of
$0.01 per share shall constitute a class designated as Preferred Stock. Shares
of Preferred Stock may be issued in one or more series from time to time. The
Board of Directors is expressly authorized to fix by resolution or resolutions
the designations and the powers, preferences and rights, and the qualifications,
limitations and restrictions of the shares of each series of Preferred Stock
(with respect to each series of Preferred Stock, the "Preferred Stock
Designation").

     FIFTH.   The Board of Directors is expressly authorized to adopt, amend or
repeal any bylaws of the Corporation by resolutions duly adopted by a majority
of the directors then in office, but the stockholders entitled to vote may adopt
additional bylaws and may amend or repeal any bylaw whether or not adopted by
them at a meeting duly called for that purpose by the affirmative vote of the
holders of not less than eighty percent (80%) of the voting power of all
outstanding shares of capital stock of the Corporation entitled to vote
generally in the election of directors, considered for purposes hereof as a
single class.

     SIXTH.   Elections of directors need not be by written ballot except and to
the extent provided in the bylaws of the Corporation.

     SEVENTH. The number of directors constituting the entire Board of Directors
shall be not less than three (3) nor more than fifteen (15), as may be fixed
from time to time by resolutions duly adopted by the Board of Directors. The
directors of the Corporation shall be divided into three classes, designated
"Class I," "Class II," and "Class III." The number of directors in each of Class
I, Class II and Class III shall be equal or as nearly equal as possible. The
term of office of the Class I directors shall expire at the 2004 annual meeting
of stockholders, the term of office of the Class II directors shall expire at
the 2005 annual meeting of stockholders, and the term of office of the Class III
directors shall expire at the 2006 annual meeting of stockholders, with each
director to hold office until his or her successor shall have been duly elected
and qualified or until his or her earlier resignation or removal. At each annual
meeting of stockholders, directors elected to succeed the directors whose terms
expire at such annual meeting commencing with the 2004 annual meeting shall be
elected to hold office for a term to expire at the third succeeding annual
meeting of stockholders following the year of their

                                      - 2 -

<PAGE>

election and until their successors have been duly elected and qualified or
until their earlier resignation or removal. If the number of directors is
changed, any increase or decrease shall be apportioned among Class I, Class II
and Class III so as to maintain the number of directors in each class as nearly
equal as possible.

A director may only be removed from office for cause and by the affirmative vote
of the holders of not less than eighty percent (80%) of the voting power of all
outstanding shares of capital stock of the Corporation entitled to vote
generally in the election of directors, considered for purposes hereof as a
single class. Except as otherwise provided pursuant to the provisions of the
Certificate of Incorporation of the Corporation (including any Preferred Stock
Designation), newly created directorships resulting from any increase in the
number of directors and any vacancies on the Board of Directors resulting from
death, resignation, disqualification, removal or other cause shall be filled by
the affirmative vote of a majority of the directors then in office, even if less
than a quorum, or by a sole remaining director in office. Any director elected
in accordance with the preceding sentence shall hold office for the remainder of
the full term of the class of directors in which the new directorship was
created or the vacancy occurred and until such director's successor shall have
been duly elected and qualified or until his or her earlier resignation or
removal. No decrease in the number of directors constituting the Board of
Directors shall shorten the term of any incumbent director.

     EIGHTH.  Except as otherwise provided pursuant to provisions of the
Certificate of Incorporation of the Corporation (including any Preferred Stock
Designation) fixing the powers, privileges or rights of any class or series of
stock other than the Common Stock in respect of action by written consent of the
holders of such class or series of stock, after Merck & Co., Inc., a New Jersey
corporation ("Merck"), ceases to be the sole stockholder of the Corporation, any
action required or permitted to be taken by the stockholders of the Corporation
must be effected at a duly called annual or special meeting of such holders and
may not be effected by any consent in writing by such holders.

     Except as otherwise provided pursuant to provisions of the Certificate of
Incorporation of the Corporation (including any Preferred Stock Designation)
fixing the powers, privileges or rights of any class or series of stock other
than the Common Stock, special meetings of stockholders of the Corporation of
any class or series of capital stock for any purpose or purposes may be called
only by the Chairman of the Board of Directors, the President, the Chief
Executive Officer of the Corporation or a majority of the Board of Directors
pursuant to a resolution stating the purpose or purposes thereof, and any power
of stockholders to call a special meeting is specifically denied, and no
business other than that stated in the notice shall be transacted at any special
meeting.

     NINTH.   A director of the Corporation shall not be liable to the
Corporation or its stockholders for monetary damages for breach of fiduciary
duty as a director, except to the extent that such exemption from liability or
limitation thereof is not permitted under the DGCL as currently in effect or as
the same may hereafter be amended. If the DGCL is amended after the effective
date of this Certificate of Incorporation of the Corporation to authorize
corporate action further eliminating or limiting the personal liability of
directors, then the liability of a director of

                                      - 3 -

<PAGE>

the Corporation shall be eliminated or limited to the fullest extent permitted
by the DGCL, as so amended.

     No amendment, modification or repeal of this Article NINTH shall adversely
affect any right or protection of a director with respect to events occurring
prior to such amendment, modification or repeal.

     TENTH.   Certain Transactions With Merck & Co., Inc.

     No contract, agreement, arrangement or transaction (or any amendment,
modification or termination thereof) entered into between the Corporation or any
of its Affiliated Companies, on the one hand, and Merck, or any of its
Affiliated Companies, on the other hand, before the Corporation ceased to be a
wholly owned subsidiary of Merck shall be void or voidable or be considered to
be unfair to the Corporation for the reason that Merck or any of its Affiliated
Companies, are parties thereto, or because directors or officers of Merck or any
of its Affiliated Companies were present at or participated in any meeting of
the Board of Directors or committee thereof which authorized the contract,
agreement, arrangement or transaction (or the amendment, modification or
termination thereof), or because his, her or their votes were counted for such
purpose. No such contract, agreement, arrangement or transaction (or the
amendment, modification or termination thereof) or the performance thereof by
the Corporation or any of its Affiliated Companies shall be considered to be
contrary to any fiduciary duty owed to the Corporation or to any stockholder of
the Corporation by any director or officer of the Corporation or of any of its
Affiliated Companies (including directors or officers of the Corporation or its
Affiliated Companies who may have been directors or officers of Merck or any of
its Affiliated Companies) and such directors and officers of the Corporation or
any of its Affiliated Companies shall be deemed to have acted in good faith and
in a manner such persons reasonably believe to be in or not opposed to the best
interests of the Corporation and shall be deemed not to have breached their
duties of loyalty to the Corporation or its stockholders, and not to have
derived an improper personal benefit therefrom. No director, officer or employee
of the Corporation or any of its Affiliated Companies shall have or be under any
fiduciary duty to the Corporation to refrain from acting on behalf of the
Corporation or any of its Affiliated Companies in respect of any such contract,
agreement, arrangement or transaction (or the amendment, modification or
termination thereof) or to refrain from performing any such contract, agreement,
arrangement or transaction (or the amendment, modification or termination
thereof) in accordance with its terms.

     Any person purchasing or otherwise acquiring any shares of capital stock of
the Corporation, or any interest therein, shall be deemed to have notice of and
to have consented to the provisions of this Article TENTH. The failure of any
contract, agreement, arrangement or transaction (or the amendment, modification
or termination thereof) between the Corporation or any of its Affiliated
Companies, on the one hand, and Merck or any of its Affiliated Companies, on the
other hand, to satisfy the requirements of this Article TENTH shall not, by
itself, cause such contract, agreement, arrangement or transaction (or the
amendment, modification or termination thereof) to constitute any breach of any
fiduciary duty to the Corporation, or to any stockholder by any director,
officer or employee of the Corporation.

                                      - 4 -

<PAGE>

     For purposes of this Article TENTH, "Affiliated Company" shall mean in
respect of Merck, any company which is controlled by Merck, controls Merck or is
under common control with Merck (other than the Corporation and any company that
is controlled by the Corporation), and in respect of the Corporation shall mean
any company controlled by the Corporation.

     In addition to any other affirmative vote or written consent required by
applicable law, this Article TENTH may not be amended, modified or repealed
except by the affirmative vote of the holders of not less than eighty percent
(80%) of the voting power of all outstanding shares of stock of the Corporation
entitled to vote generally in the election of directors, considered for purposes
hereof as a single class. Notwithstanding the foregoing, the amendment or
removal of this Article TENTH shall not terminate the effect of the provisions
hereof with respect to any contract, agreement, arrangement or transaction (or
the amendment, modification or termination thereof) between the Corporation or
any of its Affiliated Companies, on the one hand, and Merck or any of its
Affiliated Companies, on the other hand, that was entered into before the
Corporation ceased to be a wholly owned subsidiary of Merck.


                                      - 5 -

<PAGE>

     IN WITNESS WHEREOF, Medco Health Solutions, Inc. has caused this Second
Amended and Restated Certificate of Incorporation to be duly executed by an
authorized officer of Medco Health Solutions, Inc. as of this 31st day of July,
2003.

                                        MEDCO HEALTH SOLUTIONS, INC.


                                        By:  /s/ David S. Machlowitz
                                            ------------------------------------
                                        Name:  David S. Machlowitz
                                        Title: Senior Vice President, General
                                               Counsel and Secretary

                                      - 6 -