Mark Linn-Baker was born with the given names Mark Linn and the surname Baker in St. Louis, Missouri. He later changed his surname to a compound surname by hyphenating his middle name Linn with his surname Baker, producing Linn-Baker. His mother, Joan (née Sparks), was a dancer, and his father, William Nelson Baker, co-founded the Open Stage Theater in Hartford. His parents were both active in theatre and participated in civil rights activism. He graduated from Wethersfield High School in Wethersfield, Connecticut, in 1972, and from Yale University in 1976. He then attended the Yale School of Drama, receiving a MFA in Drama in 1979, and following that, found most of his early roles on stage.

His film debut was a small part in Woody Allen’s 1979 film Manhattan. The majority of Linn-Baker’s scenes were cut from the film. Three years later, he landed a far more memorable film role partly inspired by Allen himself, playing Benjy Stone in the 1982 comedy film My Favorite Year alongside Peter O’Toole. In a manner similar to his future role in Perfect Strangers, Linn-Baker played the straight man to O’Toole’s outrageous character, Alan Swann.

He appeared in the 1983 Broadway version of the Doonesbury comic strip. He appeared in Laughter on the 23rd Floor in 1993; the 1996 revival of A Funny Thing Happened on the Way to the Forum; the 1998 Roundabout Theatre Company production of A Flea in Her Ear; the 2003 musical A Year with Frog and Toad; and the 2006 comedy Losing Louie.

Having attained success on stage and the big screen, Linn-Baker began to turn his sights toward television. In 1983, he appeared in an unsold detective show pilot called O’Malley. The following year saw a role on the television movie, The Ghost Writer, and in the summer series, The Comedy Zone. Soon, Linn-Baker was appearing in several high-profile television shows. He guest-starred on a 1984 episode of Miami Vice as Bonzo Barry and portrayed hapless office worker Phil West on a 1985 episode of Moonlighting titled “Atlas Belched”. Linn-Baker starred with Charles Kimbrough in the 1985 CBS pilot The Recovery Room, a sitcom about a bar located across from a major city hospital and its inhabitants. Airing as a special that summer, the pilot did not lead to a regular series. Between parts, Linn-Baker also appeared during this time in television commercials pitching products ranging from Kellogg’s Nutri-Grain to Kraft’s Life Savers.

On a 1992 episode of Full House, Linn-Baker played Dick Donaldson, the wealthy, snobbish cousin of Becky Donaldson Katsopolis (Lori Loughlin). In 1997, he guest starred on Family Matters as the abusive boss of Harriette Winslow (Jo Marie Payton). Linn-Baker guested three times on Hangin’ with Mr. Cooper as Larry Weeks. Additionally, he appeared on an episode of Law & Order as a strip club owner being extorted by the Mob. In a 1997 episode of Sesame Street, he had a guest role as a veterinarian examining a sick—and invisible—Barkley.

In 1995, Linn-Baker married Adrianne Lobel, the daughter of children’s book author Arnold Lobel, best known for his Frog and Toad series. They divorced after having one daughter. Linn-Baker helped adapt his father-in-law’s stories into the Tony-nominated Broadway musical A Year with Frog and Toad, in which Linn-Baker played Toad and Jay Goede played Frog. On December 29, 2012, Linn-Baker married actress Christa Justus.

Linn-Baker provided the voice for one of a quartet of aardvarks in the 2002 Sandra Boynton album Philadelphia Chickens. The other three were voiced by Joe Grifasi, Michael Gross, and Devin McEwan.

On a 2003 episode of Law & Order: Criminal Intent, he guested as an insurance investigator named Wally Stevens who displays strong Asperger’s Syndrome traits. He gets a degree of empathy from Det. Robert Goren and a number of behind-his-back snickers from Goren’s partner Alexandra Eames. His character made a return cameo appearance in the season 6 episode “Endgame”, where it was revealed Goren has kept in touch with the character through correspondence. In season 2, episode 14 (“Probability”), the last line spoken by Eames is “I’m sure he’d like a pen pal.”

In 2005, he was a regular cast member on the WB Network sitcom Twins, which was canceled after a single season. He also appeared in the 2010 film How Do You Know as Ron. In 2011, he starred in his sixth Broadway show Relatively Speaking in a one-act play by Woody Allen. He previously appeared opposite Nathan Lane in A Funny Thing Happened on the Way to the Forum. In 2016 he appeared off-Broadway as Sir Peter Teazle in The School for Scandal at the Lucille Lortel Theatre. As of 2017 he is playing the role of Carlton Miller, aide to Mayor Margaret Dutton (Lorraine Bracco) on the CBS police procedural drama Blue Bloods.

He joined his friend, fellow Yale Drama School graduate and former sidekick Lewis Black, on the audiobook version of Black’s second book Me of Little Faith where he and Black recreate The Laundry Hour, an act they did in New York City in the early 1980s. He guest-stars in several episodes of the children’s TV show The Electric Company in February–March 2009 as “Uncle Sigmund Scrambler”.

In 2009, he appeared in an episode of the U.S. version of Life on Mars, playing a character who collected women’s underwear that he later used for masturbation. In 2010, he appeared in an episode of Law & Order, “The Taxman Cometh”, as Dr. Vincent Balicheck, a physician who used controversial therapies on cancer patients which resulted in their deaths.

In 2009, he had a recurring guest-starring role in the revival of The Electric Company, and in 2017, he started a recurring role on the CBS drama Blue Bloods as Deputy NYC mayor Carlton Miller. In 2019, he appeared as Josh’s father Dave in the Unbreakable Kimmy Schmidt episode “Kimmy is in a Love Square!” Also in 2019, he appeared in Season 6 (Episode 7) of The Blacklist as entomologist Dr. Jonathan Nikkila.