Returning to New York, Whitford immersed himself in theater roles, including regional productions of Shakespearean classics and replacing Tom Hulce in the Broadway production of "A Few Good Men". With a slightly higher profile, he returned to features as a surgical resident and rival of Adrian Pasdar's in "Vital Signs", a small role in "Presumed Innocent" and a doctor in "Awakenings" (all 1990). He subsequently could be seen as Al Pacino's brother-in-law in "Scent of a Woman" (1992), as a lawyer in "Philadelphia" (1993), a sharpshooter assisting Clint Eastwood in "A Perfect World" (also 1993) and as the heir-apparent Adam Sandler must thwart in "Billy Madison" (1995). He had a major role supporting Richard Gere and Bai Ling in the political thriller "Red Corner" (1997).

The small screen has offered the actor several meaty roles, including a world-weary private eye opposite Kate Capshaw in the short-lived "Black Tie Affair" (NBC, 1993), a recurring role on "NYPD Blue" (ABC, 1994) and as a man coping with the complications of his wife's pregnancy on the Emmy-winning "Love's Labor's Lost" episode of the hit NBC series "ER" (1995). He displayed his comedic gifts as one of three divorced buddies in the ABC sitcom "The Secret Lives of Men" (1998) which unfortunately tanked with audiences. Whitford fared better as a presidential deputy chief of staff in the NBC political drama "The West Wing" (1999- ), earning an Emmy for the role in 2001 and another nomination in 2002.