<PAGE>   1
     As filed with the Securities and Exchange Commission on June 19, 1997

                                                   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)

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

                         LA JOLLA PHARMACEUTICAL COMPANY
                            1994 STOCK INCENTIVE PLAN
                              (Full Title of Plan)

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

                                 STEVEN B. ENGLE
                             CHIEF EXECUTIVE OFFICER
                             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(1)       SHARE(2)      PRICE(2)           FEE
-------------------------------------------------------------------------------------------
<S>                          <C>                  <C>         <C>                <C>    
Common Stock, $0.01 par
  value per share             500,000 shares(3)    $5.21875   $2,609,375.00      $790.72
===========================================================================================
</TABLE>

(1)  Pursuant to Rule 416(a) under the Securities Act of 1933, this Registration
     Statement also covers shares issued pursuant to antidilution provisions set
     forth in the Plan. In addition, pursuant to Rule 416(c) under the
     Securities Act of 1933, this Registration Statement also covers an
     indeterminate amount of interests to be offered or sold pursuant to the
     Plan.

(2)  Estimated solely for the purpose of calculating the registration fee
     pursuant to Rule 457(c) under the Securities Act of 1933, based upon the
     average of the high and low sale prices of the Company's Common Stock on
     the Nasdaq National Market System on June 17, 1997.

(3)  1,750,000 shares are issuable under the Plan. In addition to the 500,000
     shares registered hereby, 750,000 shares of the Company's Common Stock
     issuable under the Plan were previously registered under the Registration
     Statement on Form S-8 (Registration No. 33-82664) as filed with the
     Securities and Exchange Commission on August 11, 1994 and 500,000 shares of
     the Company's Common Stock issuable under the Plan were previously
     registered under the Registration Statement on Form S-8 (Registration No.
     333-14285) as filed with the Securities and Exchange Commission on October
     17, 1996.

================================================================================
<PAGE>   2
                                  INTRODUCTION
         
         This Registration Statement on Form S-8 is filed by La Jolla
Pharmaceutical Company, a Delaware corporation (the "Company"), to register an
additional 500,000 shares of the Company's common stock, par value $0.01 per
share, 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.

                                     PART I

              INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

         Pursuant to the instructions to Form S-8, Part I (Information Required
in the Section 10(a) Prospectus) is not filed as part of this Registration
Statement.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

         In accordance with General Instruction E to Form S-8, the contents of
the Company's 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 is incorporated herein by reference and made a part hereof.

ITEM 8.  EXHIBITS.

         Pursuant to General Instruction E, only those opinions and consents
required by Item 8 are provided, as follows.

Exhibit No.       Description
-----------       -----------

     5.1          Opinion of Gibson, Dunn & Crutcher LLP as to the legality of
                  the additional 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).

     24.1         Power of Attorney (contained on signature page hereto).



                                       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 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 June 19, 1997.


                                              LA JOLLA PHARMACEUTICAL COMPANY

                                              By: /s/ STEVEN B. ENGLE
                                                  --------------------------
                                                  Steven B. Engle
                                                  Chairman of the Board,
                                                  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                           Chairman of the Board, President and Chief         June 19, 1997
------------------------------------------                 Executive Officer
              Steven B. Engle                        (Principal Executive Officer)


/s/ WOOD C. ERWIN                                   Vice President of Finance and                June 19, 1997
------------------------------------------              Chief Financial Officer
               Wood C. Erwin                  (Principal Financial and Accounting Officer)


/s/ THOMAS H. ADAMS, PH.D.                                     Director
------------------------------------------
          Thomas H. Adams, Ph.D.                                                                 June 19, 1997


/s/ WILLIAM E. ENGBERS                                         Director
------------------------------------------
            William E. Engbers                                                                   June 19, 1997


/s/ ROBERT A. FILDES, PH.D.                                    Director
------------------------------------------
          Robert A. Fildes, Ph.D.                                                                June 19, 1997


/s/ JOSEPH STEMLER                                             Director
------------------------------------------
              Joseph Stemler                                                                     June 19, 1997


/s/ W. LEIGH THOMPSON, M.D., PH.D.                             Director
------------------------------------------
      W. Leigh Thompson, M.D., Ph.D.                                                             June 19, 1997
</TABLE>


                                       3
<PAGE>   4
                                  EXHIBIT INDEX

<TABLE>
<CAPTION>

       Exhibit No.         Description
       -----------         -----------
       <S>                 <C>              
         5.1               Opinion of Gibson, Dunn & Crutcher LLP as to the legality of the additional
                           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).

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


                                       4
[{"type": "S-8", "sequence": "1", "description": "1994 STOCK INCENTIVE PLAN", "secsgml_size_bytes": 11171}]
{"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": "333-29575", "film-number": "97626403"}, "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 June 19, 1997

                                                   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)

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

                         LA JOLLA PHARMACEUTICAL COMPANY
                            1994 STOCK INCENTIVE PLAN
                              (Full Title of Plan)

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

                                 STEVEN B. ENGLE
                             CHIEF EXECUTIVE OFFICER
                             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(1)       SHARE(2)      PRICE(2)           FEE
-------------------------------------------------------------------------------------------
Common Stock, $0.01 par
  value per share             500,000 shares(3)    $5.21875   $2,609,375.00      $790.72
===========================================================================================
(1)  Pursuant to Rule 416(a) under the Securities Act of 1933, this Registration
     Statement also covers shares issued pursuant to antidilution provisions set
     forth in the Plan. In addition, pursuant to Rule 416(c) under the
     Securities Act of 1933, this Registration Statement also covers an
     indeterminate amount of interests to be offered or sold pursuant to the
     Plan.

(2)  Estimated solely for the purpose of calculating the registration fee
     pursuant to Rule 457(c) under the Securities Act of 1933, based upon the
     average of the high and low sale prices of the Company's Common Stock on
     the Nasdaq National Market System on June 17, 1997.

(3)  1,750,000 shares are issuable under the Plan. In addition to the 500,000
     shares registered hereby, 750,000 shares of the Company's Common Stock
     issuable under the Plan were previously registered under the Registration
     Statement on Form S-8 (Registration No. 33-82664) as filed with the
     Securities and Exchange Commission on August 11, 1994 and 500,000 shares of
     the Company's Common Stock issuable under the Plan were previously
     registered under the Registration Statement on Form S-8 (Registration No.
     333-14285) as filed with the Securities and Exchange Commission on October
     17, 1996.

================================================================================
2
                                  INTRODUCTION
         
         This Registration Statement on Form S-8 is filed by La Jolla
Pharmaceutical Company, a Delaware corporation (the "Company"), to register an
additional 500,000 shares of the Company's common stock, par value $0.01 per
share, 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.

                                     PART I

              INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

         Pursuant to the instructions to Form S-8, Part I (Information Required
in the Section 10(a) Prospectus) is not filed as part of this Registration
Statement.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

         In accordance with General Instruction E to Form S-8, the contents of
the Company's 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 is incorporated herein by reference and made a part hereof.

ITEM 8.  EXHIBITS.

         Pursuant to General Instruction E, only those opinions and consents
required by Item 8 are provided, as follows.

Exhibit No.       Description
-----------       -----------

     5.1          Opinion of Gibson, Dunn & Crutcher LLP as to the legality of
                  the additional 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).

     24.1         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 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 June 19, 1997.

                                              LA JOLLA PHARMACEUTICAL COMPANY

                                              By: /s/ STEVEN B. ENGLE
                                                  --------------------------
                                                  Steven B. Engle
                                                  Chairman of the Board,
                                                  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                           Chairman of the Board, President and Chief         June 19, 1997
------------------------------------------                 Executive Officer
              Steven B. Engle                        (Principal Executive Officer)

/s/ WOOD C. ERWIN                                   Vice President of Finance and                June 19, 1997
------------------------------------------              Chief Financial Officer
               Wood C. Erwin                  (Principal Financial and Accounting Officer)

/s/ THOMAS H. ADAMS, PH.D.                                     Director
------------------------------------------
          Thomas H. Adams, Ph.D.                                                                 June 19, 1997

/s/ WILLIAM E. ENGBERS                                         Director
------------------------------------------
            William E. Engbers                                                                   June 19, 1997

/s/ ROBERT A. FILDES, PH.D.                                    Director
------------------------------------------
          Robert A. Fildes, Ph.D.                                                                June 19, 1997

/s/ JOSEPH STEMLER                                             Director
------------------------------------------
              Joseph Stemler                                                                     June 19, 1997

/s/ W. LEIGH THOMPSON, M.D., PH.D.                             Director
------------------------------------------
      W. Leigh Thompson, M.D., Ph.D.                                                             June 19, 1997
3
4
                                  EXHIBIT INDEX
Exhibit No.         Description
       -----------         -----------
5.1               Opinion of Gibson, Dunn & Crutcher LLP as to the legality of the additional
                           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).

         24.1              Power of Attorney (contained on signature page hereto).
4