Fitzgerald started his acting career in 1980, at the age of eight, when he appeared as the youngest boy in Portland Player's production of Oliver!. From that time on, he worked steadily in community theater and Maine's New Vaudeville shows. In college, he began his career as a summer apprentice at Williamstown Theater Festival. At the age of twenty-six, in 1998, he starred in his first off-Broadway show, the controversial Corpus Christi by acclaimed playwright Terrence McNally. In the same year, he also appeared in The Matchmaker by Williamstown Theatre Festival, as well as an off-Broadway staging of The Cripple of Inishmaan. During the following year, Fitzgerald appeared in the Sondheim-Weidman musical Wise Guys. He also performed in a production of Babes in Arms, produced by Encores! in the New York City Center. In 2000, Fitzgerald co-starred in the 1954 Sondheim musical Saturday Night. His performance in this show earned him his first award nomination, for the Drama Desk Award for Outstanding Featured Actor in a Musical. Also in 2000, Fitzgerald played the lead role in the one-man show Fully Committed, appearing until 2001. In 2002, Fitzgerald opened in the musical Amour, adapted from a 1943 French short story written by Marcel Aymé. He performed from October 20, 2002 until November 3, 2002. His performance earned him another nomination for the Drama Desk Award for Outstanding Featured Actor in a Musical. On October 30, 2003, Fitzgerald premiered in the musical Wicked in the role of Boq. He departed the role on January 2, 2005 and was replaced by Jeffry Kuhn. Fitzgerald was seen in Gutenberg! The Musical! directed by Alex Timbers from December 3, 2006, and ran until May 6, 2007. He appeared as the character "Igor" in the Broadway production of the Mel Brooks musical Young Frankenstein, which opened on Broadway in November 2007. For the role he received an Outer Critics Circle Award, Drama Desk Award, and a Tony Award nomination for Best Featured Actor in a Musical. Fitzgerald also played Igor in the musical's out-of-town tryouts in Seattle. During rehearsals for the show his wife gave birth to their first child, a boy named Charlie. Fitzgerald played his final performance as Igor in Young Frankenstein on November 23, 2008. Fitzgerald played the title role in the world premiere of the burlesque-style musical Minsky's, in Los Angeles, which played at the Center Theatre in Ahmanson Theatre from January 21 – March 1, 2009, and also starred his former Young Frankenstein co-star Beth Leavel. He played Og in the Broadway revival of Finian's Rainbow at the St. James Theatre. For this performance, Fitzgerald won the Drama Desk Award for Outstanding Featured Actor in a Musical. He also once more received an Outer Critics Circle Award May 2010 and a Tony Award nomination for Best Featured Actor in a Musical. He starred as Pseudolus in an all-male production of Stephen Sondheim'sA Funny Thing Happened on the Way to the Forum in his tenth season with the WilliamstownTheatre Festival. The sold-out show closed on July 11, 2010. In November 2010 to February 2011 he played Launcelot Gobbo in The Merchant of Venice on Broadway. He starred as P.T. Barnum in Barnum, revived by Cameron Mackintosh, premiering at the Chichester Festival Theatre in Chichester, West Sussex, UK from July 15 through August 31, 2013. He played the role of Amos Hart in the Broadway production of Chicago, beginning October 28, 2013. At the Williamstown Theatre Festival in July 2014 he played the role of Benny Fox in its production of June Moon. Christopher played the archangel Michael in the production of An Act of God starring Jim Parsons from May - August 2015 . In March 2016, he joined the cast of Broadway transfer Waitress, playing the role of Ogie.
On the television show Twins on The WB, Fitzgerald played the character of Neil, beginning in 2005. The show was cancelled on May 18, 2006, following the merger of The WB and UPN that created the new network The CW. He appeared in full costume as an adult Cabbage Patch doll in a Geico insurance commercial. In 2017, Fitzgerald played the role of J.J. Valentine in the Netflixlimited seriesGodless, and played children's entertainer/child trafficker Sonny Shine in the SyFyfantasyblack comedycrime series Happy!.
