<PAGE>   1
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                  FORM 10-K/A

[X]  ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934 FOR THE FISCAL YEAR ENDED DECEMBER 31, 1996

                                       OR

[ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
     EXCHANGE ACT OF 1934

                         COMMISSION FILE NUMBER 0-26244

                           SEQUANA THERAPEUTICS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

           California                                    33-0550509
(STATE OR OTHER  JURISDICTION OF            (I.R.S. EMPLOYER IDENTIFICATION NO.)
 INCORPORATION OR ORGANIZATION)

  11099 N. Torrey Pines Road, Ste. 160
         La Jolla, California                             92037
(ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)                (ZIP CODE)

                                 (619) 452-6550
              (REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE)

<TABLE>
<S>                                                                      <C>
SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:              NONE

SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:              COMMON STOCK, $.001 PAR VALUE
                                                                                (TITLE OF CLASS)
</TABLE>

            Indicate by check mark whether the registrant (1) has filed all
reports required to be filed by Section 13 or 15(d) of the Securities Exchange
Act of 1934 during the preceding 12 months (or such shorter period that the
registrant was required to file such reports and (2) has been subject to such
filing requirements for the past 90 days. Yes  X   No
                                              ---     ---

            Indicate by check mark if disclosure of delinquent filers pursuant
to Item 405 of Regulation S-K is not contained herein, and will not be
contained, to the best of registrant's knowledge, in definitive proxy or
information statements incorporated by reference in Part III of this Form 10-K
or any amendment to this Form 10-K. [ ]

            The approximate aggregate market value of the voting stock held by
non-affiliates of the registrant was $113.3 million as of March 1, 1997. Shares
of common stock held by officers and directors and by each person who owns 5% or
more of the outstanding common stock have been excluded in that such persons may
be deemed to be affiliates. This determination of affiliate status is not
necessarily a conclusive determination for other purposes.

            As of March 1, 1997, the registrant had 10,189,595 shares of common
stock outstanding.

                       DOCUMENTS INCORPORATED BY REFERENCE

Designated portions of the Registrant's Definitive Proxy Statement to be
furnished for the 1997 Annual Meeting of Shareholders are incorporated by
reference in Part III of this Form 10-K.
<PAGE>   2
 (b)   Reports on Form 8-K

          The Company did not file any reports on Form 8-K during the
             quarter ended December 31, 1996.

 (c)  Exhibits

         3.1(1)   Restated Articles of Incorporation of the Registrant

         3.3(2)   Bylaws of the Registrant, as amended to date.

         10.1(2)  Shareholder Rights Agreement, dated October 21, 1994, as
                  amended to date.

         10.2(2)  1994 Incentive Stock Plan

         10.3(2)  1995 Employee Stock Purchase Plan

         10.4(2)  1995 Director Stock Option Plan

         10.5(2)  Form of Indemnification Agreement between the Registrant and
                  its officers and directors.

         10.6(2)  Master Lease Agreement dated November 1, 1993 by and between
                  Comdisco, Inc. and Registrant.

         10.7(2)* Collaborative Research Agreement dated as of July 27, 1994 by
                  and between Registrant and Glaxo, Inc.

         10.8(1)  Expansion Lease by and between Health Science Properties, Inc.
                  and Registrant dated as of November 20, 1995.

         10.9(2)* Collaborative Research Agreement dated as of June 30, 1995 by
                  and between Registrant and Corange International, Ltd.

         10.10(2)*Collaborative Research Agreement dated as of June 12,
                  1995 by and between Registrant and Boehringer Ingelheim
                  International GmbH.

         10.11(2) Employment Agreement dated February 28, 1995 between the
                  Registrant and Kevin J. Kinsella.

         10.12(2) Consulting Agreement dated March 6, 1995 between the
                  Registrant and Irwin Lerner.

         10.13(2) Letter Agreement dated September 7, 1993 between the
                  Registrant and Timothy J.R. Harris.

         10.14(3)*Research Agreement dated as of April 2, 1996 by and between
                  the Registrant and Aurora Biosciences Corporation.

         10.15(4) Merger Agreement and Plan of Reorganization between the
                  Registrant, Sequana Merger Sub, Inc., NemaPharm, Inc. and the
                  Shareholders of NemaPharm, Inc. dated July 19, 1996.

         10.16    Loan Agreement between the Registrant and The Sumitomo Bank,
                  Limited dated as of October 23, 1996.

         11.1(1)  Computation of net loss per share.

         23.1     Consent of Ernst & Young LLP, Independent Auditors.

         24.1     Power of Attorney (see page 46).

         27.1     Financial Data Schedule.

----------------

*        Confidential treatment has been granted with respect to certain
         portions of this exhibit.





                                                                              44
<PAGE>   3
(1)      Incorporated by reference to exhibits filed with Registrant's
         Registration Statement on Form S-1 (Reg. No. 333-01226).

(2)      Incorporated by reference to exhibits filed with Registrant's
         Registration Statement on Form S-1 (Reg. No. 33-93460).

(3)      Incorporated by reference to the exhibit of the same number to the
         Registrant's Quarterly Report on Form 10-Q for the Quarter ended June
         30, 1996.

(4)      Incorporated by reference to the exhibit of the same number to the
         Registrant's Quarterly Report on Form 10-Q for the Quarter ended
         September 30, 1996.




                                                                              45
<PAGE>   4
                               EXPLANATORY NOTE

            This Annual Report on Form 10-K/A is being filed as Amendment No.1
to the Registrant's Annual Report on Form 10-K filed with the Securities and
Exchange Commission on March 31, 1997 soley for the purpose of refiling Exhibit
10.16 with certain non-confidential portions in such Exhibit unredacted.


                                   SIGNATURES

            Pursuant to the requirements of Section 13 or 15(d) of the
Securities Exchange Act of 1934, as amended, the Registrant has duly caused this
Report to be signed on its behalf by the undersigned, thereunto duly authorized.

                                           SEQUANA THERAPEUTICS, INC.


                                           BY: /s/ M. SCOTT SALKA
                                               --------------------------------
                                                 M. SCOTT SALKA
                                                 VICE PRESIDENT, OPERATIONS
                                                 AND CHIEF EXECUTIVE OFFICER
DATE:  July 28, 1997


                                                                             46
<PAGE>   5
                                  EXHIBIT INDEX


<TABLE>
<CAPTION>
 Exhibit                                                                       Sequentially
 Number       Description of Document                                          Numbered Page
 ------       -----------------------                                          -------------

<S>      <C>                                                                    <C>
3.1(1)   Restated Articles of Incorporation of the Registrant

3.3(2)   Bylaws of the Registrant, as amended to date.

10.1(2)  Shareholder Rights Agreement, dated October 21, 1994, as amended to
         date.

10.2(2)  1994 Incentive Stock Plan

10.3(2)  1995 Employee Stock Purchase Plan

10.4(2)  1995 Director Stock Option Plan

10.5(2)  Form of Indemnification Agreement between the Registrant and its
         officers and directors.

10.6(2)  Master Lease Agreement dated November 1, 1993 by and between Comdisco,
         Inc. and Registrant.

10.7(2)* Collaborative Research Agreement dated as of July 27, 1994 by and
         between Registrant and Glaxo, Inc.

10.8(1)  Expansion Lease by and between Health Science Properties, Inc. and
         Registrant dated as of November 20, 1995.

10.9(2)* Collaborative Research Agreement dated as of June 30, 1995 by and
         between Registrant and Corange International, Ltd.

10.10(2)*Collaborative Research Agreement dated as of June 12, 1995 by and
         between Registrant and Boehringer Ingelheim International GmbH.

10.11(2) Employment Agreement dated February 28, 1995 between the Registrant and
         Kevin J. Kinsella.

10.12(2) Consulting Agreement dated March 6, 1995 between the Registrant and
         Irwin Lerner.

10.13(2) Letter Agreement dated September 7, 1993 between the Registrant and
         Timothy J.R. Harris.

10.14(3)*Research Agreement dated as of April 2, 1996 by and between the
         Registrant and Aurora Biosciences Corporation.

10.15(4) Merger Agreement and Plan of Reorganization between the Registrant,
         Sequana Merger Sub, Inc., NemaPharm, Inc. and the Shareholders of
         NemaPharm, Inc. dated July 19, 1996.

10.16    Loan Agreement between the Registrant and The Sumitomo Bank, Limited
         dated as of October 23, 1996.

11.1(1)  Computation of net loss per share.

23.1     Consent of Ernst & Young LLP, Independent Auditors.

24.1     Power of Attorney (see page 46).

27.1     Financial Data Schedule.
</TABLE>

----------------

*        Confidential treatment has been granted with respect to certain
         portions of this exhibit.



                                                                              48
<PAGE>   6
(1)      Incorporated by reference to exhibits filed with Registrant's
         Registration Statement on Form S-1 (Reg. No. 333-01226).

(2)      Incorporated by reference to exhibits filed with Registrant's
         Registration Statement on Form S-1 (Reg. No. 33-93460).

(3)      Incorporated by reference to the exhibit of the same number to the
         Registrant's Quarterly Report on Form 10-Q for the Quarter ended June
         30, 1996.

(4)      Incorporated by reference to the exhibit of the same number to the
         Registrant's Quarterly Report on Form 10-Q for the Quarter ended
         September 30, 1996.

                                                                              49