Emerson was born in Cedar Rapids, Iowa and grew up in the nearby town of Toledo, Iowa. He attended South Tama County High School. After graduating in 1976 from Drake University in Des Moines, Iowa, where he studied theater and art, he moved to New York City. Unable to find acting work, he took retail jobs and worked as a freelance illustrator. In 1986, he moved with his first wife to Jacksonville, Florida. There, from 1986 to 1993, he appeared in local productions at Theater Jacksonville and The Players by the Sea, and worked as a director and teacher at Flagler College.

Emerson considered forgoing a career in acting in favor of a more stable vocation in teaching. He decided to instead further his studies with a Master of Fine Arts that might also introduce him to theatre professionals and directors in his chosen trade. In 1993 he enrolled in the Alabama Shakespeare Festival's University of Alabama-sponsored Master of Fine Arts/Professional Actor Training program, and upon graduating in 1995, he returned to New York where he appeared in the annual Alabama Shakespeare Festival showcase.

Emerson got his big break in 1997 when he starred as Oscar Wilde in Moises Kaufman's critically acclaimed off-Broadway play, Gross Indecency: The Trials of Oscar Wilde, and then followed up with several other notable stage performances. In 1998, he performed opposite Uma Thurman in the off-Broadway production of Le Misanthrope. In 1999, he played the part of Willie Oban in The Iceman Cometh with Kevin Spacey. He co-starred with Kate Burton in both Give Me Your Answer, Do! and Hedda Gabler.

In film and television, Emerson made a name for himself by playing dangerous and damaged characters. In 2001, he won an Emmy Award as "Outstanding Guest Actor in a Drama Series", for playing the (fictional) confessed serial killer William Hinks in several episodes of The Practice.

One of Emerson's best known works was in 2004 as the character Zep Hindle in the horror movie Saw. In that year he also played the loyal, somewhat Alfred Pennyworth-like butler to a Rock Hudson-like heartthrob, Guy Stone, in the comedy film Straight-Jacket.

In 2006, Emerson began a guest-star role playing Benjamin Linus on the serial drama television series Lost. This casting was a result of his work on The Practice because the Lost producers liked his work there and thought he was a good fit for the character they were developing. Emerson was originally set to appear in a small number of episodes, then returned for the third season as a main cast member and eventually became the main antagonist of the program. He has since continued to be a main cast member on the show for the fourth and fifth seasons and has recently finished working on the sixth season. Emerson's performance and character have been highly acclaimed by critics and audiences. He received an Emmy nomination in the "Outstanding Supporting Actor" category in 2007 for his work on the series' third season and was nominated again in 2008 for the fourth season. He won the award in 2009 after being nominated for the fifth season. Emerson was nominated in 2009 for a Golden Globe in the "Best Performance by an Actor in a Supporting Role" category.

Emerson met the woman who was to become his second wife, actress Carrie Preston, while he was performing in a stage production of Hamlet in Alabama. They married in September 1998, and both Emerson and his wife starred in the 2004 film Straight-Jacket. On Lost, Preston portrayed Emily Linus, Emerson's character's mother, in the flashback sequences of the episode "The Man Behind the Curtain". The two teamed up again, with Emerson playing Preston's gay next-door neighbor, in the 2008 film Ready? OK!. According to a recent interview, Emerson is also interested in joining Preston on the TV series True Blood, where she plays waitress Arlene, for a guest appearance.

He is a long-time supporter of the charities connected to the theatre community, including the Actors Fund, Broadway Cares, Gay Men's Health Crisis, and Off-Off Broadway, in addition to publicly supported radio stations and Habitat.

Michael Emerson (2001) · Charles S. Dutton (2002) · Charles S. Dutton (2003) · William Shatner (2004) · Ray Liotta (2005) · Christian Clemenson (2006) · John Goodman (2007) · Glynn Turman (2008) · Michael J. Fox (2009)

Complete list: (1975–2000) · (2001–present)