<PAGE>   1

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                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                            ------------------------

                                AMENDMENT NO. 1
                                       TO


                                  FORM 10-K/A

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

(MARK ONE)

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


                    FOR THE FISCAL YEAR ENDED JUNE 30, 1998


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


              FOR THE TRANSITION PERIOD FROM ____________ TO ____________
                            COMMISSION FILE NUMBER: 0-15086

                                 SUN MICROSYSTEMS, INC.
                 (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

<TABLE>
<S>                                            <C>
                   DELAWARE                                      94-2805249
           (STATE OF INCORPORATION)                 (I.R.S. EMPLOYER IDENTIFICATION NO.)
             901 SAN ANTONIO ROAD
             PALO ALTO, CA 94303                               (650) 960-1300
   (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES,
              INCLUDING ZIP CODE)                           INCLUDING AREA CODE)
</TABLE>

             SECURITIES PURSUANT TO SECTION 12(B) OF THE ACT: NONE
          SECURITIES REGISTERED PURSUANT TO SECTION 12(G) OF THE ACT:
                                  COMMON STOCK
                          COMMON SHARE PURCHASE RIGHTS

    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 for 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 the Registrant's knowledge, in definitive proxy or information
statements incorporated by reference on Part III of this Form 10-K or any
amendment to this Form 10-K   [ ].

    The aggregate market value of the voting stock held by non-affiliates of the
Registrant, as of September 15, 1998, was approximately $18,682,000,000 based
upon the last sale price reported for such date on the Nasdaq National Market.
For purposes of this disclosure, shares of Common Stock held by persons who hold
more than 5% of the outstanding shares of Common Stock and shares held by
officers and directors of the Registrant have been excluded because such persons
may be deemed to be affiliates. This determination is not necessarily
conclusive.

    The number of shares of the Registrant's Common Stock outstanding as of
September 15, 1998 was 381,262,063.

                      DOCUMENTS INCORPORATED BY REFERENCE

    Parts of the Annual Report to Stockholders for the fiscal year ended June
30, 1998 are incorporated by reference into Items 1, 5, 6, 7, 8 and 14 hereof.

    Parts of the Proxy Statement for the 1998 Annual Meeting of Stockholders are
incorporated by reference into Items 10, 11, 12 and 13 hereof.
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<PAGE>   2

ITEM 14. EXHIBITS, FINANCIAL STATEMENTS, SCHEDULES AND REPORTS ON FORM 8-K

(a) The following documents are filed as part of this report:

     1. Financial statements that are incorporated herein by reference to the
        following in Sun's 1998 Annual Report to Stockholders.

      Consolidated Statements of Income for each of the three years in the
      period ended June 30, 1998 (page 26).

       Consolidated Balance Sheets at June 30, 1998 and 1997 (page 27).

       Consolidated Statements of Cash Flows for each of the three years in the
       period ended June 30, 1998 (page 28).

       Consolidated Statements of Stockholders' Equity for each of the three
       years in the period ended June 30, 1998 (page 29).

       Notes to Consolidated Financial Statements (pages 30 through 43).

       Report of Ernst & Young LLP, Independent Auditors (page 44).

     The Company's 1998 Annual Report to Stockholders is not deemed filed as
part of this report except for those parts specifically incorporated herein by
reference.

3. Exhibits

<TABLE>
<CAPTION>
 EXHIBIT
 NUMBER                            DESCRIPTION
 -------                           -----------
<S>        <C>
 3.1(11)   Registrant's Restated Certificate of Incorporation, as
           amended February 12, 1998.
 3.2(11)   Registrant's Bylaws, as amended February 11, 1998.
 4.8(12)   Second Amended and Restated Shares Rights Agreement dated as
           of February 11, 1998.
10.1(1)    Technology Transfer Agreement dated February 27, 1982, for
           the purchase by the Registrant of certain technology for
           cash, and related Assumption Agreement dated February 27,
           1982.
10.3(1)    Form of Founders' Restricted Stock Purchase Agreement.
10.8(1)    Registration Rights Agreement dated as of November 26, 1984.
10.8A(1)   Amendment to Registration Rights Agreement.
10.9(2)    Registrant's 1982 Stock Option Plan, as amended, and
           representative forms of Stock Option Agreement.
10.10(2)   Registrant's Restricted Stock Plan, as amended, and
           representative form of Stock Purchase Agreement.
10.11(4)   Registrant's 1984 Employee Stock Purchase Plan, as amended.
10.21(1)   License Agreement dated July 26, 1983, by and between
           Registrant and The Regents of the University of California.
10.22(1)   Software Agreement effective as of April 1, 1982 by and
           between Registrant and American Telephone and Telegraph
           Company, and Supplemental Agreement dated effective as of
           May 28, 1983.
10.48(2)   Registrant's 1987 Stock Option Plan and representative form
           of Stock Option Agreement.
10.56(3)   Building Loan Agreement dated May 11, 1989, between Sun
           Microsystems Properties, Inc. and the Toyo Trust and Banking
           Company Limited, New York Branch and the related Promissory
           Note; First Deed of Trust, Assignment of Leases, Rents and
           Other Income and Security Agreement; Guaranty of Payment;
           Guaranty of Completion (Sun Microsystems Properties, Inc.);
           Guaranty of Completion (Sun Microsystems, Inc.; Shortfall
           Agreement and Indemnity.
</TABLE>

                                        1
<PAGE>   3

<TABLE>
<CAPTION>
 EXHIBIT
 NUMBER                            DESCRIPTION
 -------                           -----------
<S>        <C>
10.64(10)  Registrant's 1988 Directors' Stock Option Plan as amended on
           August 13, 1997.
10.65(10)  Registrant's 1990 Employee Stock Purchase Plan, as amended
           on August 13, 1997.
10.66(6)   Registrant's 1990 Long-Term Equity Incentive Plan, as
           amended on August 15, 1996.
10.66A(5)  Representative form of agreement to Registrant's 1990
           Long-Term Equity Incentive Plan.
10.74(5)   Software Distribution Agreement dated January 28, 1991 by
           and between the Registrant and UNIX Systems Laboratories,
           Inc.
10.82(9)   Revolving Credit Agreement dated August 28, 1997, between
           the Registrant; Citicorp USA, Inc.; Bank of America National
           Trust and Savings Association; ABN AMRO Bank N.V.; The First
           National Bank of Boston; Barclays Bank PLC; Morgan Guaranty
           Trust Company of New York; The Fuji Bank Limited, San
           Francisco Agency: The Toyo Trust and Banking Co. Ltd.: The
           Sumitomo Bank, Limited; The Sakura Bank Limited, San
           Francisco Agency; Banque Nationale de Paris; Bayerische
           Vereinsbank AG, Los Angeles Agency; The Industrial Bank of
           Japan, Limited, San Francisco Agency; The Bank of New York;
           Cariplo -- Cassa Di-Risparmio Delle Provincie Lombade SPA;
           Corestes Bank NA; The Northern Trust Company; Royal Bank Of
           Canada; Union Bank of California, N.A.; and The Sumitomo
           Trust Banking Co., Ltd.
10.84*     Registrant's Non-Qualified Deferred Compensation Plan, as
           amended July 1, 1998.
10.85(7)   Registrant's Section 162 (m) Executive Officer
           Performance-Based Bonus Plan dated August 9, 1995.
10.87(9)   Registrant's Equity Compensation Acquisition Plan, as
           amended on August 28, 1997.
10.89(8)   Form of Change of Control Agreement executed by each
           corporate executive officer of Registrant.
10.90(8)   Form of Change of Control Agreement executed by Chief
           Executive Officer of Registrant.
10.91(8)   Form of Vice President Change of Control Severance Plan.
10.92(8)   Form of Director-Level Change of Control Severance Plan.
13.0       Registrant's 1998 Annual Report to Stockholders (to be
           deemed filed only to the extent required by the instructions
           to exhibits for reports on Form 10-K).
21.0*      Subsidiaries of Registrant.
23.1       Consent of Ernst & Young LLP, Independent Auditors.
24*        Power of Attorney.
27*        Financial Data Schedule.
</TABLE>

---------------
  *  Previously filed.

 (1) Incorporated by reference to the Registrant's Registration Statement on
     Form S-1 (No. 33-2897), which became effective March 4, 1986.

 (2) Incorporated by reference to Exhibits 19.1, 19.3 or 19.4, filed as Exhibits
     to the Registrant's Quarterly Report on Form 10-Q for the quarter ended
     December 25, 1987.

 (3) Incorporated by reference to identically numbered exhibits filed as
     exhibits to the Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1989.

 (4) Incorporated by reference to Exhibit 4.1 filed as an Exhibit to
     Registrant's Registration Statement on Form S-8 file number 33-38220, filed
     with the Securities and Exchange Commission on December 14, 1990.

 (5) Incorporated by reference to identically numbered exhibits filed as
     exhibits to the Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1991.

 (6) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1996.

                                        2
<PAGE>   4

 (7) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1995.

 (8) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Quarterly Report on Form 10-Q for the quarter
     ended December 29, 1996.

 (9) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1997.

(10) Incorporated by reference to Exhibits 4.2 and 4.1, respectively filed as
     exhibits to Registrant's Registration Statement on Form S-8 file number
     333-40677, filed with the Securities and Exchange Commission on November
     20, 1997.

(11) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Quarterly Report on Form 10-Q for the quarter
     ended March 29, 1998.

(12) Incorporated herein by reference to the Registrant's Registration Statement
     on Form 8-A/A Amendment No. 6 filed on February 13, 1998.

                                        3
<PAGE>   5

                                   SIGNATURES

     Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the registrant has duly caused this Amendment No. 1 to the
Annual Report to be signed on its behalf by the undersigned, thereunto duly
authorized.

                                          SUN MICROSYSTEMS, INC.
                                          Registrant

June 14, 1999


                                                 /s/ MICHAEL E. LEHMAN
                                          --------------------------------------
                                                    Michael E. Lehman
                                           Vice President, Corporate Resources
                                               and Chief Financial Officer

                                        4
<PAGE>   6

     Pursuant to the requirements of the Securities Exchange Act of 1934, this
Amendment No. 1 to the Annual Report has been signed below by the following
persons, which include the Chief Executive Officer, the Chief Financial Officer
and Corporate Controller and a majority of the Board of Directors, on behalf of
the registrant and in the capacities and on the dates indicated.


<TABLE>
<CAPTION>
              SIGNATURE                                 TITLE                       DATE
              ---------                                 -----                       ----
<C>                                     <S>                                     <C>

                  *                     Chairman of the Board of Directors,     June 14, 1999
--------------------------------------    President and Chief Executive
          (Scott G. McNealy)              Officer (Principal Executive
                                          Officer)

        /s/ MICHAEL E. LEHMAN           Vice President, Corporate Resources     June 14, 1999
--------------------------------------    and Chief Financial Officer
         (Michael E. Lehman)              (Principal Financial Officer)

         /s/ MICHAEL L. POPOV           Vice President and Corporate            June 14, 1999
--------------------------------------    Controller (Principal Accounting
          (Michael L. Popov)              Officer)

                  *                     Director                                June 14, 1999
--------------------------------------
           (L. John Doerr)

                  *                     Director                                June 14, 1999
--------------------------------------
          (Judith L. Estrin)

                  *                     Director                                June 14, 1999
--------------------------------------
          (Robert J. Fisher)

                  *                     Director                                June 14, 1999
--------------------------------------
           (Robert L. Long)

                  *                     Director                                June 14, 1999
--------------------------------------
         (M. Kenneth Oshman)

                  *                     Director                                June 14, 1999
--------------------------------------
         (A. Michael Spence)

       * /s/ MICHAEL E. LEHMAN
--------------------------------------
          Michael E. Lehman
         (Power of Attorney)
</TABLE>


                                        5
<PAGE>   7

INDEX TO EXHIBITS

<TABLE>
<CAPTION>
 EXHIBIT
 NUMBER                            DESCRIPTION
 -------                           -----------
<S>        <C>
 3.1(11)   Registrant's Restated Certificate of Incorporation, as
           amended February 12, 1998.
 3.2(11)   Registrant's Bylaws, as amended February 11, 1998.
 4.8(12)   Second Amended and Restated Shares Rights Agreement dated as
           of February 11, 1998.
10.1(1)    Technology Transfer Agreement dated February 27, 1982, for
           the purchase by the Registrant of certain technology for
           cash, and related Assumption Agreement dated February 27,
           1982.
10.3(1)    Form of Founders' Restricted Stock Purchase Agreement.
10.8(1)    Registration Rights Agreement dated as of November 26, 1984.
10.8A(1)   Amendment to Registration Rights Agreement.
10.9(2)    Registrant's 1982 Stock Option Plan, as amended, and
           representative forms of Stock Option Agreement.
10.10(2)   Registrant's Restricted Stock Plan, as amended, and
           representative form of Stock Purchase Agreement.
10.11(4)   Registrant's 1984 Employee Stock Purchase Plan, as amended.
10.21(1)   License Agreement dated July 26, 1983, by and between
           Registrant and The Regents of the University of California.
10.22(1)   Software Agreement effective as of April 1, 1982 by and
           between Registrant and American Telephone and Telegraph
           Company, and Supplemental Agreement dated effective as of
           May 28, 1983.
10.48(2)   Registrant's 1987 Stock Option Plan and representative form
           of Stock Option Agreement.
10.56(3)   Building Loan Agreement dated May 11, 1989, between Sun
           Microsystems Properties, Inc. and the Toyo Trust and Banking
           Company Limited, New York Branch and the related Promissory
           Note; First Deed of Trust, Assignment of Leases, Rents and
           Other Income and Security Agreement; Guaranty of Payment;
           Guaranty of Completion (Sun Microsystems Properties, Inc.);
           Guaranty of Completion (Sun Microsystems, Inc.; Shortfall
           Agreement and Indemnity.
10.64(10)  Registrant's 1988 Directors' Stock Option Plan as amended on
           August 13, 1997.
10.65(10)  Registrant's 1990 Employee Stock Purchase Plan, as amended
           on August 13, 1997.
10.66(6)   Registrant's 1990 Long-Term Equity Incentive Plan, as
           amended on August 15, 1996.
10.66A(5)  Representative form of agreement to Registrant's 1990
           Long-Term Equity Incentive Plan.
10.74(5)   Software Distribution Agreement dated January 28, 1991 by
           and between the Registrant and UNIX Systems Laboratories,
           Inc.
10.82(9)   Revolving Credit Agreement dated August 28, 1997, between
           the Registrant; Citicorp USA, Inc.; Bank of America National
           Trust and Savings Association; ABN AMRO Bank N.V.; The First
           National Bank of Boston; Barclays Bank PLC; Morgan Guaranty
           Trust Company of New York; The Fuji Bank Limited, San
           Francisco Agency: The Toyo Trust and Banking Co. Ltd.: The
           Sumitomo Bank, Limited; The Sakura Bank Limited, San
           Francisco Agency; Banque Nationale de Paris; Bayerische
           Vereinsbank AG, Los Angeles Agency; The Industrial Bank of
           Japan, Limited, San Francisco Agency; The Bank of New York;
           Cariplo -- Cassa Di-Risparmio Delle Provincie Lombade SPA;
           Corestes Bank NA; The Northern Trust Company; Royal Bank Of
           Canada; Union Bank of California, N.A.; and The Sumitomo
           Trust Banking Co., Ltd.
10.84*     Registrant's Non-Qualified Deferred Compensation Plan, as
           amended July 1, 1998.
10.85(7)   Registrant's Section 162 (m) Executive Officer
           Performance-Based Bonus Plan dated August 9, 1995.
</TABLE>
<PAGE>   8

<TABLE>
<CAPTION>
 EXHIBIT
 NUMBER                            DESCRIPTION
 -------                           -----------
<S>        <C>
10.87(9)   Registrant's Equity Compensation Acquisition Plan, as
           amended on August 28, 1997.
10.89(8)   Form of Change of Control Agreement executed by each
           corporate executive officer of Registrant.
10.90(8)   Form of Change of Control Agreement executed by Chief
           Executive Officer of Registrant.
10.91(8)   Form of Vice President Change of Control Severance Plan.
10.92(8)   Form of Director-Level Change of Control Severance Plan.
13.0       Registrant's 1998 Annual Report to Stockholders (to be
           deemed filed only to the extent required by the instructions
           to exhibits for reports on Form 10-K).
21.0*      Subsidiaries of Registrant.
23.1       Consent of Ernst & Young LLP, Independent Auditors.
24*        Power of Attorney.
27*        Financial Data Schedule.
</TABLE>

---------------
  *  Previously filed.

 (1) Incorporated by reference to the Registrant's Registration Statement on
     Form S-1 (No. 33-2897), which became effective March 4, 1986.

 (2) Incorporated by reference to Exhibits 19.1, 19.3 or 19.4, filed as Exhibits
     to the Registrant's Quarterly Report on Form 10-Q for the quarter ended
     December 25, 1987.

 (3) Incorporated by reference to identically numbered exhibits filed as
     exhibits to the Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1989.

 (4) Incorporated by reference to Exhibit 4.1 filed as an Exhibit to
     Registrant's Registration Statement on Form S-8 file number 33-38220, filed
     with the Securities and Exchange Commission on December 14, 1990.

 (5) Incorporated by reference to identically numbered exhibits filed as
     exhibits to the Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1991.

 (6) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1996.

 (7) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1995.

 (8) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Quarterly Report on Form 10-Q for the quarter
     ended December 29, 1996.

 (9) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Annual Report on Form 10-K for the fiscal year
     ended June 30, 1997.

(10) Incorporated by reference to Exhibits 4.2 and 4.1, respectively filed as
     exhibits to Registrant's Registration Statement on Form S-8 file number
     333-40677, filed with the Securities and Exchange Commission on November
     20, 1997.

(11) Incorporated by reference to identically numbered exhibits filed as
     exhibits to Registrant's Quarterly Report on Form 10-Q for the quarter
     ended March 29, 1998.

(12) Incorporated herein by reference to the Registrant's Registration Statement
     on Form 8-A/A Amendment No. 6 filed on February 13, 1998.