MacNicol won the 2001 Primetime Emmy Award for Outstanding Supporting Actor in a Comedy Series for his role as the eccentric lawyer John Cage in the FOX comedy-drama Ally McBeal (1997–2002). He is also known for his television roles as attorney Alan Birch in the medical drama Chicago Hope (1994–98), Tom Lennox in the sixth season of action-thriller 24 (2007), as physicist Dr. Larry Fleinhardt on the CBS crime drama Numbers (2005–10), Armadillo Dave on All Grown Up! (2007), Dr. Stark on Grey's Anatomy (2010–11), Jeff Kane on the political satire series Veep (2016–17), and Nigel the Advisor on Tangled: The Series.
MacNicol was born and raised in Dallas, Texas, the youngest of five children of Barbara Jean (née Gottlich), a homemaker, and John Wilbur Johnson, a Norwegian-American corporate executive who became an Episcopal priest later in life.
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.
According to the casting sheet, which can be seen at 8:22 in the documentary 'The making of Amadeus', he was being considered for the role of Mozart in Milos Forman's film.
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.
Among his other stage credits is the Broadway production of Black Comedy/White Lies. He has further extensive classical repertory theater background, including the New York Shakespeare Festival in which he played title roles in Richard II and Romeo and Juliet, and appeared in Twelfth Night, Rum and Coke and Found a Peanut.
On film, he played the naive Southern writer who fell in love with Meryl Streep in Sophie's Choice, the museum curator Janosz Poha in Ghostbusters II, and camp director Gary Granger alongside future Numbers co-star David Krumholtz in Addams Family Values. Other film credits include Housesitter and American Blue Note.
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".
MacNicol has lent his voice to several comic book supervillains: Dr. Kirk Langstrom/Man-Bat in The Batman, David Clinton/Chronos in Justice League Unlimited, Professor Ivo in Young Justice, Dr. Otto Octavius/Doctor Octopus in The Spectacular Spider-Man, X The Eliminator in Harvey Birdman, Attorney at Law and the Mad Hatter in the video games Batman: Arkham City, Batman: Arkham Origins, and Batman: Arkham Knight. He also voiced Firefly in G.I. Joe: Renegades., and He is voiced "Armadillo Dave" in All Grown Up!.
MacNicol played Dr. Stark, a pediatric surgeon, on Grey's Anatomy.
MacNicol was nominated for an Emmy for outstanding guest actor in the fifth season of Veep; however, this was rescinded after he appeared for all of ten seconds in a fifth episode of the season's ten episode run, hence disqualifying him as a part-time "guest" and joining him in the ranks of Dennis Miller and Henry Winkler whose nominations were also revoked.