<PAGE>   1
      As filed with the Securities and Exchange Commission on June 6, 1996

                                                       Registration No. 333-____

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

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
                                   ----------
                                    FORM S-3
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933
                                   ----------
                        IDEC PHARMACEUTICALS CORPORATION
             (Exact name of Registrant as specified in its charter)

                CALIFORNIA                              33-0112644      
      (State or other jurisdiction                   (I.R.S. Employer        
   of incorporation or organization)                Identification No.)
                                                     
                11011 Torreyana Rd., San Diego, California 92121
                                 (619) 550-8500
   (Address, including zip code, and telephone number, including area code,
                  of Registrant's principal executive offices)

                           William H. Rastetter, Ph.D.
                      President and Chief Executive Officer
                        IDEC PHARMACEUTICALS CORPORATION
                11011 Torreyana Rd., San Diego, California 92121
                                 (619) 550-8500
            (Name, address, including zip code, and telephone number,
                   including area code, of agent for service)
                                   ----------
                                   Copies to:

       J. Stephan Dolezalek, Esq.           Robert V. Gunderson, Jr., Esq.
       Faye H. Russell, Esq.                Jay K. Hachigian, Esq.
       BROBECK, PHLEGER & HARRISON LLP      GUNDERSON DETTMER STOUGH VILLENEUVE
       Two Embarcadero Place                  FRANKLIN & HACHIGIAN, LLP
       2200 Geng Road                       600 Hansen Way, Second Floor
       Palo Alto, California 94303          Palo Alto, California  94304
       (415) 424-0160                       (415) 843-0500
                                   ----------

                  APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED
                SALE TO THE PUBLIC: As soon as practicable after
                 this Registration Statement becomes effective.

     If the only securities being registered on this form are being offered
pursuant to dividend or interest reinvestment plans, please check the following
box: [ ]

     If any of the securities being registered on this form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box: [ ]

     If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering: [x] 333-4424

     If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]

     If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box: [ ]

                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>
====================================================================================================================================
                                                                           PROPOSED            PROPOSED
                                                        AMOUNT              MAXIMUM             MAXIMUM                  AMOUNT OF
            TITLE OF EACH CLASS OF                       TO BE          OFFERING PRICE         AGGREGATE               REGISTRATION
          SECURITIES TO BE REGISTERED              REGISTERED(1)(2)        PER UNIT        OFFERING PRICE(3)              FEE (4)

- -----------------------------------------------------------------------------------------------------------------------------------
<S>                                                 <C>                     <C>               <C>                          <C>   
Common Stock, no par value.....................     345,000 shares          $24.00            $8,280,000                   $2,856
====================================================================================================================================
</TABLE>

(1) Includes 45,000 shares of Common Stock that the Underwriters have the option
    to purchase to cover over-allotments, if any.
(2) Shares of Common Stockpreviously registered include 1,725,000 shares for
    which the registration fee has previously been paid.
(3) The proposed maximum offering price per share is based on the proposed
    offering price for the shares of the Company's Common Stock offered
    hereby.
(4) Calculated pursuant to Rule 457.



<PAGE>   2



                INCORPORATION OF CERTAIN INFORMATION BY REFERENCE

         This Registration Statement filed under the Securities Act of 1933, as
amended, by IDEC Pharmaceuticals Corporation (the "Company") with the Securities
and Exchange Commission (the "Commission") hereby incorporates by reference the
contents of the Registration Statement on Form S-3 (File No. 333-4424) relating
to the offering of up to 1,725,000 Shares of Common Stock of the Company filed
on May 3, 1996, as amended through the date hereof.

                                  CERTIFICATION

         The Company hereby certifies to the Commission that it has instructed
its bank to pay the Commission the filing fee of $2,856 for the additional
securities being registered hereby as soon as practicable (but in any event no
later than the close of business on June 7, 1996); that it will not revoke such
instructions; that it has sufficient funds in the relevant account to cover the
amount of the filing fee; and that it undertakes to confirm receipt of such
instructions by the bank on June 7, 1996.



<PAGE>   3






                                   SIGNATURES

      Pursuant to the requirements of the Securities Act of 1933, the Company
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-3 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on the 6th day of
June, 1996.

                                       IDEC PHARMACEUTICALS CORPORATION


                                       By: /s/ WILLIAM H. RASTETTER
                                           ------------------------
                                           William H. Rastetter
                                           President and Chief Executive Officer

      Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.


<TABLE>
<CAPTION>
         Signature                                                          Title                            Date

               *                                                                                          
<S>                                                       <C>                                             <C>    
- ---------------------------------------                   President and Chief Executive Officer and       June 6, 1996
     (William H. Rastetter)                                Director (Principal Executive Officer)


               *                                                                                          June 6, 1996
- ---------------------------------------                       Vice President and Chief Financial
     (Philip M. Schneider)                                    Officer (Principal Financial and
                                                                     Accounting Officer)


               *                                                          Director                        June 6, 1996
- ---------------------------------------
     (Charles C. Edwards, M.D.)


               *                                                          Director                        June 6, 1996
- ---------------------------------------
          (John Groom)


               *                                                          Director                        June 6, 1996
- ---------------------------------------
      (Kazuhiro Hashimoto)


               *                                                          Director                        June 6, 1996
- ---------------------------------------
       (Peter Barton Hutt)


               *                                                          Director                        June 6, 1996
- ---------------------------------------
     (Franklin P. Johnson, Jr.)


               *                                                           Director                       June 6, 1996
- ---------------------------------------
       (John P. McLaughlin)


- ---------------------------------------                                    Director                             , 1996
          (Lynn Schenk)
          

/s/ WILLIAM H. RASTETTER                                                                                  June 6, 1996
- ---------------------------------------                                  
      William H. Rastetter
       Attorney-in-Fact
</TABLE>




<PAGE>   4



                                  EXHIBIT INDEX


<TABLE>
<CAPTION>
   Exhibit                                                                              Sequentially
     No.                                  Description                                   Numbered Page
- ------------                              -----------                                 -----------------
<S>        <C>                                                                        <C>       
    5.1    Opinion of Brobeck, Phleger & Harrison LLP with respect to the Common
               Stock being registered.

   23.1    Consent of Brobeck, Phleger & Harrison LLP (contained in their
               opinion filed as Exhibit 5.1).

   23.2    Independent Auditors' Consent, KPMG Peat Marwick LLP
  +24.1    Power of Attorney.
</TABLE>

- -----------------------
+ Incorporated by reference to the same-numbered exhibit to the Company's
  Registration Statement on Form S-3 (No. 333-4424) filed on May 3, 1996.







<PAGE>   1



                                                                     EXHIBIT 5.1

                   OPINION OF BROBECK, PHLEGER & HARRISON LLP

                                  June 6, 1996

IDEC Pharmaceuticals Corporation
11011 Torreyana Road
San Diego, California 92121

     Re:      345,000 Shares of Common Stock of IDEC Pharmaceuticals Corporation

Ladies and Gentlemen:

                  We have acted as counsel to IDEC Pharmaceuticals Corporation,
a California corporation (the "Company"), in connection with the proposed
issuance and sale by the Company of up to 345,000 shares of the Company's Common
Stock (the "Shares"), pursuant to the Company's Registration Statement on Form
S-3 (the "Registration Statement").

                  In connection with this opinion, we have examined the
Registration Statement and related Prospectus, the Company's Articles of
Incorporation, as amended through the date hereof, the Company's bylaws, as
amended through the date hereof, and the originals, or copies certified to our
satisfaction, of such records, documents, certificates, memoranda and other
instruments as in our judgment are necessary or appropriate to enable us to
render the opinion expressed below (the "Documents"). We are relying (without
any independent investigation thereof) upon the truth and accuracy of the
statements, covenants, representations and warranties set forth
 in such
Documents.

                  On the basis of the foregoing, and in reliance thereon, we are
of the opinion that the Shares have been duly authorized, and if, as and when
issued in accordance with the Registration Statement and Prospectus (as amended
and supplemented through the date of issuance) will be validly issued, fully
paid and nonassessable.

                  We consent to the use of this opinion as an exhibit to the
Registration Statement and further consent to all references to us in the
Registration Statement, the Prospectus and any further amendments thereto.
Subject to the foregoing sentence, this opinion is given as of the date hereof
solely for your benefit and may not be relied upon, circulated, quoted or
otherwise referred to for any purpose without our prior written consent.

                                       Very truly yours,


                                       BROBECK, PHLEGER & HARRISON LLP





<PAGE>   1



                                                                    EXHIBIT 23.1

                   CONSENT OF BROBECK, PHLEGER & HARRISON LLP

                           (Contained in Exhibit 5.1)







<PAGE>   1
 
                                                                    EXHIBIT 23.2
 
                               [KPMG LETTERHEAD]
 
                         INDEPENDENT AUDITORS' CONSENT
 
The Board of Directors
IDEC Pharmaceuticals Corporation:
 
     We consent to the use of our report included herein and our reports
incorporated herein by reference and to the references to our firm under the
headings "Experts" and "Selected Consolidated Financial Data" in the prospectus.
 
                                          KPMG PEAT MARWICK LLP

San Diego, California
June 5, 1996