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 also.
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 a main antagonist of the program. He has since continued to be a main cast member on the show for the fourth and fifth seasons, his character slowly morphing from a villain to an antihero, 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. He was nominated for Emmys for each season in which he was listed in the main cast.
Emerson met the woman who was to become his second wife, actress Carrie Preston (graduate of the prestigious drama programs from The University of Evansville and Juilliard), 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.
On July 31, 2010, Michael Emerson and his wife Carrie Preston (Arlene Fowler of HBO's True Blood) read A. R. Gurney's Love Letters, which was nominated for a Pulitzer Prize for Drama, at the Charleston Stage. They performed it as a fundraiser for the South Carolina's theatre. The reading was followed by a brief and intimate Question and Answer session.
With Steve Carell leaving The Office after its seventh season, it is rumoured Michael Emerson may be a candidate to replace Carell on the show.
He is set to reunite with former "Lost" cast member and friend, Terry O'Quinn in a comedic-drama, tentatively titled Odd Jobs, by J.J Abrams. It is expected to start filming by the end of 2010. Airing will most likely be in early 2011.
In 2011, Michael Emerson started to play the protagonist in a CBS Drama show Person Of Interest. A Drama that has to do with the government having a device that sees all crimes that people do. The character, whose name is Finch, that Michael Emerson plays is the owner and inventor of this device. This show continues to this day.
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.
He has been married to the US actress Carrie Preston since 1998. 
|1998||The Impostors||Burtom's Assistant|
|Playing by Heart||Bosco|
|1999||For Love of the Game||Gallery Doorman|
|2002||The Laramie Project||Reverend|
|2005||29th and Gay||Gorilla|
|The Legend of Zorro||Harrigan|
|2006||Jumping Off Bridges||Frank Nelson|
|2008||Ready? OK!||Charlie New|
|2010||Goldstar, Ohio||Steve Harper|
|1990||Orpheus Descending||Clown||TV movie|
|1998||Grace & Glorie||Arnold Dudley||TV movie|
|2000||The District||Man in Bar||Episode: "Pilot"|
|2000–2001||The Practice||William Hinks||6 episodes|
|2001||The Education of Max Bickford||Unknown role||Episode: "Herding Carts"|
|Sounds from a Town I Love||Unknown role||TV movie|
|2002||Law & Order: Criminal Intent||Gerry Rankin||Episode: "Phantom"|
|The X-Files||Oliver Martin||Episode: "Sunshine Days"|
|2003||Without a Trace||Stuart Wesmar||Episode: "Victory for Humanity"|
|Skin||Scarpelli||Episode: "Secrets & Lies"|
|Whoopi||F. Thomas Erickson||Episode: "The Fat and the Frivolous"|
|2004||Law & Order: Special Victims Unit||Allan Shaye||Episode: "Ritual"|
|2005||The Inside||Marty Manning||Episode: "Pre-Filer"|
|2006–2010||Lost||Ben Linus||76 episodes|
|2011 - ?||Odd Jobs||TBA|
- Othello, University of North Florida
- Noises Off (as Gary), Theatre Jacksonville, 1986 or 1987
- Romeo and Juliet, Shakespeare at the Met, 1987
- The Importance of Being Earnest, Arkansas Repertory Theatre, 1990
- Parts Unknown, Players-By-The-Sea Theatre, Jacksonville Beach, Florida, 1993
- Hamlet (as Hamlet), Players-By-The-Sea Theatre, Jacksonville Beach, Florida
- The Tempest (as Ferdinand), Alabama Shakespeare Festival, 1994 or 1995
- The Way of the World (as Lady Wishfort), Alabama Shakespeare Festival, 1994 or 1995
- Hamlet (as Rosencrantz), Alabama Shakespeare Festival, 1994 or 1995
- All's Well That Ends Well, Alabama Shakespeare Festival, 1994 or 1995
- Henry IV, Part 1, Alabama Shakespeare Festival, 1994 or 1995
- A Christmas Carol, Alabama Shakespeare Festival, 1994 or 1995
- The Crucible, Alabama Shakespeare Festival, 1994 or 1995
- Amadeus, Arkansas Repertory Theatre, 1995
- Androcles and the Lion, Alabama Shakespeare Festival, 1995 or 1996
- Gross Indecency: The Trials of Oscar Wilde (as Oscar Wilde), Minetta Lane Theatre, off-Broadway, 1997–1998
- The Misanthrope, Classic Stage Company, 1998
- The Iceman Cometh (as Willie Oban), Brooks Atkinson Theatre, 1999
- Give Me Your Answer, Do! (as David Knight), Gramercy Theatre, off-Broadway, 1999–2000
- Hedda Gabler (as George Tesman), Williamstown Theatre Festival, Main Stage, 2000
- Hedda Gabler (as George Tesman), Ambassador Theatre, Broadway, 2001–2002
- Only the End of the World (as Louis), Theatre 3, off-Broadway, 2002
- Frequency Hopping (as George Antheil), Hourglass Group, 2002
- Tartuffe (as Cleante), American Airlines Theatre, Broadway, 2003
- Measure for Measure (as Duke Vincentio), California Shakespeare Theater, Orinda, California, 2003
- Someone Who'll Watch Over Me, The Ridgefield Playhouse for Movies and the Performing Arts, 2004
- Hamlet (as Ghost, Claudius, Osric, and Guildenstern), McCarter Theatre Center, Princeton, New Jersey, 2005
- Bach at Leipzig (as Schott), New York Theatre Workshop, 2005
- Likeness, Primary Stages Theater (307 W. 38th Street), 2008
- Every Good Boy Deserves Favour (as Alexander), Chautauqua Theater Company, 2008
- Love Letters (as Andrew Makepeace Ladd, III), Charleston Stage, 2010
- Participated in a staged reading of a play involving string theory written by Jacquelyn Reingold called String Fever at Rockefeller University in 2003.
- Played the unnamed narrator character in the radio play adaptation of the Neil Gaiman short story, Murder Mysteries.
- The audio book version of James Patterson's novel, Four Blind Mice, which he co-narrated with Peter J. Fernandez.
- Private Sector, audio book of the novel by Brian Haig, which he co-narrated with John Rubinstein.
- Narrated the Neil Gaiman American Gods novella The Monarch of the Glen (from Fragile Things) in volume III of an audio book series called "Legends II: New Short Novels by the Masters of Modern Fantasy" .
- Narrated audio book CD of Robert Penn Warren's novel All the King's Men in 2005.
- Narrated audio book CD of The Amalgamation Polka by Stephen Wright, published in February 2006.
- Was the voice of George Washington in Favorite Son, a 2003 experimental documentary film about the relationship between George Washington and Alexander Hamilton.
- Participated in a Woody Allen short called "Sounds From a Town I Love" which aired on television during The Concert for New York City in 2001 and depicts people talking on their cellphones as they walk around New York City.
- With other Lost cast members, he participated in a play-reading session in February 2007 at the Tenney Theatre in Hawaii to raise money for the Honolulu Theatre for Youth.
- Narrated a reading of "Babar the Elephant" with the Honolulu Symphony Orchestra, in 2009.
- Won an Emmy at the 53rd Primetime Emmy Awards (Outstanding Guest Actor in a Drama Series) for playing "William Hinks" on The Practice, 2001.
- Nominated for an Emmy at the 59th Primetime Emmy Awards (Outstanding Supporting Actor in a Drama Series) for portraying Ben Linus on LOST, 2007.
- Nominated for an Emmy at the 60th Primetime Emmy Awards (Outstanding Supporting Actor in a Drama Series) for portraying Ben Linus on LOST, 2008.
- Won an Emmy at the 61st Primetime Emmy Awards (Outstanding Supporting Actor in a Drama Series) for portraying Ben Linus on LOST, 2009.
- Nominated for a Golden Globe at the 67th Golden Globe Awards (Best Performance by an Actor in a Supporting Role in a Series, Mini-Series or Motion Picture Made for Television) for portraying Ben Linus on LOST, 2010.
- Won a Saturn Award at the 34th Saturn Awards (Best Supporting Television Actor) for portraying Ben Linus on LOST, 2008.
- Nominated for a Saturn Award at the 35th Saturn Awards (Best Supporting Television Actor) for portraying Ben Linus on LOST, 2009.
- Nominated for a Saturn Award at the 36th Saturn Awards (Best Supporting Television Actor) for portraying Ben Linus on LOST, 2010.
- Nominated for an Emmy at the 62nd Primetime Emmy Awards (Outstanding Supporting Actor in a Drama Series) for portraying Ben Linus on LOST, 2010