MacNicol performed for two seasons from 1978 at the Guthrie Theater in Minneapolis, including in productions of Hamlet and The Pretenders. He made his New York debut in the 1980 off-Broadway play, Crimes of the Heart. The production eventually moved to Broadway in 1981, and he won the Theatre World Award. It was also during this production that a casting agent noticed him and called him in to read for his eventual role in Sophie's Choice. In 1981 he landed the starring role in his first film, Dragonslayer, opposite Sir Ralph Richardson.
In 1987, he starred in the Trinity Repertory Company's original production of the stage adaptation of All the King's Men, which first appeared at the Dallas Theater Center. This adaptation was developed with the consultation of the author himself.
From 1992-1993 he starred opposite John Forsythe, Holland Taylor, David Hyde Pierce and Joseph Gordon-Levitt as press secretary Bradley Grist in the short-lived political comedy The Powers that Be.
In 1994 MacNicol had a prominent role as Alan Birch for the first season and under half of the second season of Chicago Hope before departing to take on a role on another TV series, Ally McBeal, also created by Chicago Hope's creator, David E. Kelley. However, he did return for one final guest appearance in episode five of the former show's fifth season.
MacNicol is known by television viewers for his Ally McBeal performance as eccentric attorney John Cage, for which he won an Emmy Award for Outstanding Supporting Actor in a Comedy Series in 2001. He also starred in the drama Numbers as Physicist Dr. Larry Fleinhardt, and had a role as Tom Lennox in the sixth season of the hit FOX show 24. MacNicol reprised his role as Lennox in the film 24: Redemption. He also played a hotel receptionist in one episode of Cheers titled "Look Before You Sleep".
