<PAGE>   1

    As filed with the Securities and Exchange Commission on October 17, 1996

                                                Registration No. 333-________
=============================================================================


                       SECURITIES AND EXCHANGE COMMISSION                     
                            WASHINGTON, D.C. 20549 
                            
                             ----------------------
                            
                                    FORM S-8
                            
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                        
                        
                        LA JOLLA PHARMACEUTICAL COMPANY
------------------------------------------------------------------------------
            (Exact name of Registrant as specified in its charter)


             DELAWARE                                     33-0361285
  -------------------------------                     -------------------
  (State or other jurisdiction of                      (I.R.S. Employer
   incorporation or organization)                     Identification No.)


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

                             6455 NANCY RIDGE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (619) 452-6600
              (Address, including zip code, and telephone number,
       including area code, of Registrant's Principal Executive Offices)
                           
                             ----------------------
                           
                           1994 STOCK INCENTIVE PLAN
                             (Full Title of Plan)  
                                                          
                             ----------------------
                                                           
                                STEVEN B. ENGLE
                            CHIEF EXECUTIVE OFFICER
                        LA JOLLA PHARMACEUTICAL COMPANY
                             6455 NANCY RIDGE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (619) 452-6600
            (Name, address, including zip code, and telephone number, 
                   including area code, of agent for service)
                   
                             ----------------------
                   
                        CALCULATION OF REGISTRATION FEE
<TABLE>
<CAPTION>
==============================================================================================================
                                                              PROPOSED           PROPOSED                                      
                                                               MAXIMUM            MAXIMUM                                      
                                            AMOUNT            OFFERING           AGGREGATE        AMOUNT OF                    
         TITLE OF SECURITIES                TO BE             PRICE PER          OFFERING        REGISTRATION                  
           TO BE REGISTERED               REGISTERED          SHARE(1)           PRICE(1)            FEE                       
--------------------------------------------------------------------------------------------------------------  
 <S>                                    <C>                     <C>             <C>                <C>                         
  COMMON STOCK, $.01 PAR VALUE          500,000 SHARES          $4.50           $2,250,000         $681.82                     
==============================================================================================================
</TABLE>

(1)  Estimated solely for the purpose of calculating the registration fee
     pursuant to Rules 457(h) and 457(c) and based on the high and low prices 
     of the Common Stock of La Jolla Pharmaceutical Company as reported on 
     October 14, 1996 on the NASDAQ National Market System.

=============================================================================



                                       1
<PAGE>   2
                                  INTRODUCTION
                                  
         This Registration Statement on Form S-8 is filed by La Jolla
Pharmaceutical Company, a Delaware corporation (the "Company") relating to an
additional 500,000 shares of the Company's common stock, par value $.01 per
share (the "Common Stock"), issuable under the Company's 1994 Stock Incentive
Plan (the "Plan"), and consists of only those items required by General
Instruction E to Form S-8.


            INCORPORATION OF PREVIOUSLY FILED REGISTRATION STATEMENT

         The contents of the Registration Statement on Form S-8, Registration
No. 33-82664, previously filed by the Company with the Securities and Exchange
Commission on August 11, 1994, are incorporated herein by reference and made a
part hereof.


ITEM 8.  EXHIBITS.

<TABLE>
<S>      <C>

4.1      Restated Certificate of Incorporation of the Company (filed as 
         Exhibit 3.3 to the Company's Annual Report on Form 10-K for the fiscal
         year ended December 31, 1994, and incorporated herein by reference)

4.2      Bylaws for the Regulation of the Company (filed as Exhibit 3.2 to the
         Company's Registration Statement on Form S-1 (No. 33-76480), and
         incorporated herein by reference)

5        Opinion of Gibson, Dunn & Crutcher LLP as to the legality of the 
         securities being registered

23.1     Consent of Ernst & Young LLP, independent auditors

23.2     Consent of Gibson, Dunn & Crutcher LLP (contained in Exhibit 5 hereto)

24       Power of Attorney (contained on signature page hereto)
</TABLE>




                                       2
<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 a filing on Form S-8 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 September 30, 
1996.


                                             LA JOLLA PHARMACEUTICAL COMPANY
                                             
                                             
                                             By:  /s/ STEVEN B. ENGLE
                                             --------------------------------
                                                      Steven B. Engle
                                                      President and Chief 
                                                      Executive Officer


                               POWER OF ATTORNEY

         Each person whose signature appears below constitutes and appoints
STEVEN B. ENGLE and WOOD C. ERWIN his true and lawful attorneys-in-fact and
agents, each acting alone, with full powers of substitution and resubstitution,
for him and in his name, place and stead, in any and all capacities, to sign any
and all amendments (including post-effective amendments) to this Registration
Statement and to file the same, with all exhibits thereto, and other documents
in connection therewith, with the Securities and Exchange Commission, granting
unto said attorneys-in-fact and agents, each acting alone, with full powers and
authority to do and perform each and every act and thing requisite and necessary
to be done in and about the premises, as full to all intents and purposes as he
might or could do in person, hereby ratifying and confirming that all said
attorneys-in-fact and agents, each acting alone, or his substitute or
substitutes, may lawfully do or cause to be done by virtue hereof.  

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

<TABLE>
<CAPTION>

           Signature                                           Title                               Date
           ---------                                           -----                               ----
      <S>                                   <C>                                              <C>

/s/  STEVEN B. ENGLE                            President, Chief Executive Officer           September 30, 1996
---------------------------------                 (Principal Executive Officer)                              
     Steven B. Engle                                      and Director         
                                                  
                              
/s/  WOOD C. ERWIN                          Vice President-Finance, Secretary and Chief      September 30, 1996
---------------------------------             Financial Officer (Principal Financial 
     Wood C. Erwin                                    and Accounting Officer)           
                                                                                      

/s/  JOSEPH STEMLER                                    Chairman of the Board                 September 30, 1996
---------------------------------                                                                                     
     Joseph Stemler             
              
                      
/s/  THOMAS H. ADAMS                                         Director                        September 30, 1996
---------------------------------                                                                                    
     Thomas H. Adams, Ph.D.     

    
/s/  WILLIAM E. ENGBERS                                      Director                        September 30, 1996
---------------------------------                                                                                   
     William E. Engbers       

    
/s/  ROBERT A. FILDES                                        Director                        September 30, 1996
---------------------------------                                                                                    
     Robert A. Fildes, Ph.D.    

    
/s/  W. LEIGH THOMPSON, M.D.                                 Director                        September 30, 1996
---------------------------------                                                                                
 W. Leigh Thompson, M.D., Ph.D.     
</TABLE>





                                       3
<PAGE>   4
                                 EXHIBIT INDEX
<TABLE>
<CAPTION>

 Exhibit No.       Description                                                                              
 -----------       -----------                                                                              
    <S>            <C>                                                                                      
    4.1*           Restated Certificate of Incorporation of the Company                                     
                                                                                                            
    4.2*           Bylaws for the Regulations of the Company                                                
                                                                                                            
    5              Opinion of Gibson, Dunn & Crutcher LLP as to the legality of the securities being        
                   registered                                                                               
                                                                                                            
    23.1           Consent of Ernst & Young LLP, independent auditors                                       
                                                                                                            
    23.2           Consent of Gibson, Dunn & Crutcher LLP (contained in Exhibit 5 hereto)                   
                                                                                                            
    24             Power of Attorney (contained on signature page hereof)                                   
</TABLE>

----------------
*  Incorporated herein by reference.  See sequentially numbered page 2.




                                       4
[{"type": "S-8", "sequence": "1", "description": "FORM S-8 AS FILED ON OCTOBER 17, 1996", "secsgml_size_bytes": 12502}]
{"company-data": {"conformed-name": "LA JOLLA PHARMACEUTICAL CO", "cik": "0000920465", "assigned-sic": "2836", "irs-number": "330361285", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-14285", "film-number": "96644619"}, "business-address": {"street1": "6455 NANCY RIDGE DR", "city": "SAN DIEGO", "state": "CA", "zip": "92121", "phone": "6194526600"}, "mail-address": {"street1": "6455 NANCY RIDGE DR", "city": "SAN DIEGO", "state": "CA", "zip": "92121"}}
1

    As filed with the Securities and Exchange Commission on October 17, 1996

                                                Registration No. 333-________
=============================================================================

                       SECURITIES AND EXCHANGE COMMISSION                     
                            WASHINGTON, D.C. 20549 
                            
                             ----------------------
                            
                                    FORM S-8
                            
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                        
                        
                        LA JOLLA PHARMACEUTICAL COMPANY
------------------------------------------------------------------------------
            (Exact name of Registrant as specified in its charter)

             DELAWARE                                     33-0361285
  -------------------------------                     -------------------
  (State or other jurisdiction of                      (I.R.S. Employer
   incorporation or organization)                     Identification No.)

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

                             6455 NANCY RIDGE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (619) 452-6600
              (Address, including zip code, and telephone number,
       including area code, of Registrant's Principal Executive Offices)
                           
                             ----------------------
                           
                           1994 STOCK INCENTIVE PLAN
                             (Full Title of Plan)  
                                                          
                             ----------------------
                                                           
                                STEVEN B. ENGLE
                            CHIEF EXECUTIVE OFFICER
                        LA JOLLA PHARMACEUTICAL COMPANY
                             6455 NANCY RIDGE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (619) 452-6600
            (Name, address, including zip code, and telephone number, 
                   including area code, of agent for service)
                   
                             ----------------------
                   
                        CALCULATION OF REGISTRATION FEE
==============================================================================================================
                                                              PROPOSED           PROPOSED                                      
                                                               MAXIMUM            MAXIMUM                                      
                                            AMOUNT            OFFERING           AGGREGATE        AMOUNT OF                    
         TITLE OF SECURITIES                TO BE             PRICE PER          OFFERING        REGISTRATION                  
           TO BE REGISTERED               REGISTERED          SHARE(1)           PRICE(1)            FEE                       
--------------------------------------------------------------------------------------------------------------
COMMON STOCK, $.01 PAR VALUE          500,000 SHARES          $4.50           $2,250,000         $681.82                     
==============================================================================================================
(1)  Estimated solely for the purpose of calculating the registration fee
     pursuant to Rules 457(h) and 457(c) and based on the high and low prices 
     of the Common Stock of La Jolla Pharmaceutical Company as reported on 
     October 14, 1996 on the NASDAQ National Market System.

=============================================================================

                                       1
2
                                  INTRODUCTION
                                  
         This Registration Statement on Form S-8 is filed by La Jolla
Pharmaceutical Company, a Delaware corporation (the "Company") relating to an
additional 500,000 shares of the Company's common stock, par value $.01 per
share (the "Common Stock"), issuable under the Company's 1994 Stock Incentive
Plan (the "Plan"), and consists of only those items required by General
Instruction E to Form S-8.

            INCORPORATION OF PREVIOUSLY FILED REGISTRATION STATEMENT

         The contents of the Registration Statement on Form S-8, Registration
No. 33-82664, previously filed by the Company with the Securities and Exchange
Commission on August 11, 1994, are incorporated herein by reference and made a
part hereof.

ITEM 8.  EXHIBITS.
4.1      Restated Certificate of Incorporation of the Company (filed as 
         Exhibit 3.3 to the Company's Annual Report on Form 10-K for the fiscal
         year ended December 31, 1994, and incorporated herein by reference)

4.2      Bylaws for the Regulation of the Company (filed as Exhibit 3.2 to the
         Company's Registration Statement on Form S-1 (No. 33-76480), and
         incorporated herein by reference)

5        Opinion of Gibson, Dunn & Crutcher LLP as to the legality of the 
         securities being registered

23.1     Consent of Ernst & Young LLP, independent auditors

23.2     Consent of Gibson, Dunn & Crutcher LLP (contained in Exhibit 5 hereto)

24       Power of Attorney (contained on signature page hereto)
2
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 a filing on Form S-8 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 September 30, 
1996.

                                             LA JOLLA PHARMACEUTICAL COMPANY
                                             
                                             
                                             By:  /s/ STEVEN B. ENGLE
                                             --------------------------------
                                                      Steven B. Engle
                                                      President and Chief 
                                                      Executive Officer

                               POWER OF ATTORNEY

         Each person whose signature appears below constitutes and appoints
STEVEN B. ENGLE and WOOD C. ERWIN his true and lawful attorneys-in-fact and
agents, each acting alone, with full powers of substitution and resubstitution,
for him and in his name, place and stead, in any and all capacities, to sign any
and all amendments (including post-effective amendments) to this Registration
Statement and to file the same, with all exhibits thereto, and other documents
in connection therewith, with the Securities and Exchange Commission, granting
unto said attorneys-in-fact and agents, each acting alone, with full powers and
authority to do and perform each and every act and thing requisite and necessary
to be done in and about the premises, as full to all intents and purposes as he
might or could do in person, hereby ratifying and confirming that all said
attorneys-in-fact and agents, each acting alone, or his substitute or
substitutes, may lawfully do or cause to be done by virtue hereof.  

         Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities indicated on the date indicated.
Signature                                           Title                               Date
           ---------                                           -----                               ----
/s/  STEVEN B. ENGLE                            President, Chief Executive Officer           September 30, 1996
---------------------------------                 (Principal Executive Officer)                              
     Steven B. Engle                                      and Director         
                                                  
                              
/s/  WOOD C. ERWIN                          Vice President-Finance, Secretary and Chief      September 30, 1996
---------------------------------             Financial Officer (Principal Financial 
     Wood C. Erwin                                    and Accounting Officer)           
                                                                                      

/s/  JOSEPH STEMLER                                    Chairman of the Board                 September 30, 1996
---------------------------------                                                                                     
     Joseph Stemler             
              
                      
/s/  THOMAS H. ADAMS                                         Director                        September 30, 1996
---------------------------------                                                                                    
     Thomas H. Adams, Ph.D.     

    
/s/  WILLIAM E. ENGBERS                                      Director                        September 30, 1996
---------------------------------                                                                                   
     William E. Engbers       

    
/s/  ROBERT A. FILDES                                        Director                        September 30, 1996
---------------------------------                                                                                    
     Robert A. Fildes, Ph.D.    

    
/s/  W. LEIGH THOMPSON, M.D.                                 Director                        September 30, 1996
---------------------------------                                                                                
 W. Leigh Thompson, M.D., Ph.D.
3
4
                                 EXHIBIT INDEX
Exhibit No.       Description                                                                              
 -----------       -----------
4.1*           Restated Certificate of Incorporation of the Company                                     
                                                                                                            
    4.2*           Bylaws for the Regulations of the Company                                                
                                                                                                            
    5              Opinion of Gibson, Dunn & Crutcher LLP as to the legality of the securities being        
                   registered                                                                               
                                                                                                            
    23.1           Consent of Ernst & Young LLP, independent auditors                                       
                                                                                                            
    23.2           Consent of Gibson, Dunn & Crutcher LLP (contained in Exhibit 5 hereto)                   
                                                                                                            
    24             Power of Attorney (contained on signature page hereof)
----------------
*  Incorporated herein by reference.  See sequentially numbered page 2.

                                       4