<PAGE>
 
                                                                    Exhibit 10.9

                           SECOND AMENDMENT TO LEASE

     This SECOND AMENDMENT TO LEASE (this "Second Amendment") is made this 30th
day of October, 1998, by and between TEACHERS INSURANCE & ANNUITY ASSOCIATION OF
AMERICA, INC., as successor to WRC PROPERTIES, INC. ("Landlord") and ICOS
CORPORATION ("Tenant").

                                    Recitals
                                    --------

     Landlord is landlord and Tenant is tenant under that certain Lease dated
for reference purposes December 20, 1996, as amended by First Amendment to Lease
dated August 5, 1997 (collectively the "Premier South Lease"), for premises
located at 22025 20th Avenue SE, Bothell, Washington 98021 (the "Property").
The legal description of the land on which the Property is located is attached
hereto as Exhibit A.

     Tenant wishes to add to the Property, effective February 8, 1999, an
additional agreed 25,466 Rentable Square Feet shown in crosshatching on Exhibit
B hereto (the "Expansion Property"), such that the Property shall, after such
addition, consist of an agreed 42,962 Rentable Square Feet, all as outlined in
black on Exhibit B hereto.

     Landlord has agreed to such expansion all on the terms and conditions set
forth herein.

     Except as specifically set forth herein, all capitalized terms used herein
shall have the meanings assigned in the Lease.


                                   Agreement
                                   ---------
                                        
     NOW THEREFORE, for good and valuable consideration the parties hereto agree
as follows:

     1.  On February 8, 1999, the Expansion Property shall be added to the
Property, such that the Property under Section 1.04 of the Lease shall include
all of the area outlined in black on Exhibit B and shall consist of an agreed
42,962 Rentable Square Feet.

     2.  The Project square footage as referenced in Rider 1 to the Lease dated
December 20, 1996 shall be amended to approximately 93,259 Rentable Square Feet.

     3.  Simultaneous with addition of the Expansion Property, Tenant's pro rata
share, as used to allocate all items of Additional Rent under the Lease
(including Common Area Costs pursuant to Section 4.05(e) of Rider 1 of the
Lease) shall be recalculated to reflect the addition of the Expansion Property
and Tenant's pro rata share shall thereafter be 46.07%.

     4.  Landlord shall make up to Sixty Three Thousand Six Hundred Sixty Five
Dollars ($63,665) (the "Tenant Improvement Allowance") available to Tenant to
reimburse Tenant for actual out-of-pocket costs paid to third parties for
designing and constructing tenant improvements to the Expansion Property
pursuant to plans reasonably approved by Landlord and otherwise subject to the
provisions of Section 6.05 of the Lease.  Landlord shall pay the Tenant
Improvement Allowance within thirty (30) days of invoice submitted after the
improvements have been inspected and accepted by Tenant (less minor punch list
items).  The Tenant Improvement Allowance shall be available on a one-time basis
for improvements to the Expansion Premises constructed during the past twelve
months by Tenant which were approved by Landlord.

     5.  Tenant acknowledges that it has been occupying the Expansion Premises
pursuant to a sublease, and that it accepts the Expansion Premises "as-is, where
is", and that Landlord has not made any representation regarding nor undertaken
any obligation to improve or modify the Expansion Premises.
<PAGE>
 
     6.  The Base Rent under Section 1.13 of the Lease shall be calculated
without reference to this Second Amendment until February 8, 1999 and thereafter
shall be as follows:
<TABLE>
 
               <S>                                          <C>
                February 8, 1999 to January 9, 2000     $48,229
                January 10, 2000 to February 7, 2001    $49,780
                February 8, 2001 to January 9, 2002     $52,252
                January 10, 2002 to February 7, 2003    $53,458
                February 8, 2003 to February 9, 2004    $56,133
</TABLE>

     7.  Except as specifically set forth herein, all terms and conditions of
the Lease are and remain in full force and effect.


                                       Landlord:

                                       TEACHERS INSURANCE & ANNUITY ASSOCIATION
                                       OF AMERICA, INC.

                                       By: /s/ James Garofalo
                                           -------------------------------------
                                            James Garofalo
                                       Its:  Assistant Secretary


                                       Tenant:

                                       ICOS CORPORATION

                                       By: /s/ Gary Wilcox
                                          --------------------------------------
                                           Gary Wilcox
                                       Its:  Executive Vice President/Operations
<PAGE>
 
STATE OF    New York     )
         --------------
                         )  ss.
COUNTY OF   New York     )
         --------------
 

     I certify that I know or have satisfactory evidence that James Garofalo is
the person who appeared before me, and said person acknowledged that he signed
this instrument, on oath stated that he was authorized to execute the instrument
and acknowledged it as the Assistant Secretary of Teachers Insurance & Annuity
Association of America, Inc. to be the free and voluntary act of such party for
the uses and purposes mentioned in the instrument.

                                      Dated:           12/21/98
                                            --------------------------------

                                      /s/ Marian Useloff
                                      --------------------------------------
                                      (Signature)

                                      /s/ Marian Useloff 
                                      --------------------------------------
                                      (Print Name)

                                      Notary Public, in and for the State of 
                                      NY , residing at NY County

                                      My Commission Expires 3/30/00


STATE OF WASHINGTON  )
                     )  ss.
COUNTY OF SNOHOMISH  )


     I certify that I know or have satisfactory evidence that Mr. Gary Wilcox is
the person who appeared before me, and said person acknowledged that he signed
this instrument, on oath stated that he was authorized to execute the instrument
and acknowledged it as the Executive Vice President/Operations of ICOS
Corporation to be the free and voluntary act of such party for the uses and
purposes mentioned in the instrument.

                                      Dated:           11/3/98
                                            --------------------------------

                                      /s/ Lori L. Briseno
                                      --------------------------------------
                                      (Signature)

                                      /s/ Lori L. Briseno
                                      --------------------------------------
                                      (Print Name)
                                      Notary Public, in and for the State
                                      of Washington, residing at Snohomish

                                      My Commission Expires 4/29/02
<PAGE>
 
                                   EXHIBIT A
                                (The "Premises")



To be attached.
<PAGE>
 
                                   EXHIBIT B
                           (the "Expansion Property")
                                        
Cross hatched area denotes Expansion Premises