In 1994, Mol was spotted by Photographer David william Powell. He photographed her in New York's Central Park and replaced her unrepresentative portfolio with professional-looking black-and-white images which landed her on the cover of W within weeks, and foreshadowed her "It Girl" and "Bettie Page" looks. Shortly afterwards, she ended her brief modeling career and entered acting full-time.

Mol's first television work was in a Coca-Cola commercial. Mol had a small role of Maggie Tilton in the 1996 miniseries Dead Man's Walk, based on the Larry McMurtry novel. She also was in a few episodes of Spin City. She was the star of the short-lived David E. Kelley series Girls Club (2002), a drama about three women lawyers. The series was not well received and it was cancelled after two episodes.

In 1998, she appeared in several notable films including Rounders, starring Matt Damon and Woody Allen's Celebrity opposite Leonardo DiCaprio. In 1998, she also came to prominence when she was featured on the cover of Vanity Fair, dubbed the "It Girl of the Nineties" by the magazine.

For her second film with Woody Allen, 1999's Sweet and Lowdown, she played a minor role which the Greenwich Village Gazette called "notable". She played the female lead role in the 1999 film The Thirteenth Floor. She played the victim of a con Artist in the 2003 film, Heavy Put-Away, based on the Terry Southern story. In 2006, she shared the lead in a romantic comedy, Puccini for Beginners, in which her character has a lesbian affair.

She appeared in two TV remakes of classic films: Picnic (2000), in the role of Madge Owens, and The Magnificent Ambersons as Lucy Morgan (2002). She made a Hallmark Hall of Fame television movie in January 2007, starring in The Valley of Light, a story set in post-World War II based on a novel by Terry Kay. It was her second Hallmark production. She had a minor role in Calm at Sunset in 1996.

Mol's acting career began in summer stock theatre in Vermont where she played a variety of roles including Godspell and 110 in the Shade. She played Jenny in Neil LaBute's The Shape of Things on stage in both London and New York in 2001, in a role she reprised in the film version, released in 2003. The New York Times critic Ben Brantley, in his review of the play (which he disliked), wrote, "[Mol] gives by far the most persuasive performance as the unworldly Jenny, and you wind up feeling for her disproportionately, only because she seems to be entirely there, in the present tense". In 2004, Mol spent a year singing and dancing as Roxie in the Broadway production of Chicago. In 2014–2015, Mol played the role of Emily in the Broadway debut of the Pulitzer Prize–winning Ayad Akhtar play Disgraced.

She married film Director Kip Williams on June 1, 2004. Their first child, Ptolemy John Williams, was born September 10, 2007. On February 17, 2011, Mol gave birth to their second child, daughter Winter Morgan Williams. While raising Ptolemy, Mol has only taken jobs close to her home in New York City. "I told my agent I didn't want to work in L.A., even if it was the greatest job in the world. I didn't want to compromise."

Interviewed by the Associated Press in Baltimore in December 2006, Mol commented about how she maintained her confidence as an actress: "It is an ongoing struggle. Confidence is something that sometimes you have and sometimes you don't. And the older you get, hopefully, the more you have some tools to at least fake it".

The next year, 2007, was one of her busiest, with four films in production or in release, including a remake of 3:10 to Yuma starring Russell Crowe, and An American Affair, in which her character, Catherine Caswell, has an affair with John F. Kennedy. When released in February 2009, the film was harshly criticized by New York Times critic Stephen Holden, though he said that Mol's part was "quite well acted".

She played Annie in the ABC series Life on Mars, the U.S. remake of the British show of the same name. It started airing in the U.S. on October 9, 2008 and ran 17 episodes, concluding on April 1, 2009.

Mol serves as the national spokesperson in the United States for the PMD Foundation, which funds research and awareness of Pelizaeus–Merzbacher disease, a neurological disorder afflicting children worldwide. Mol became involved with PMD after one of her cousins died from amyotrophic lateral sclerosis (familiarly known as "Lou Gehrig's Disease").

She had a recurring role on HBO's Boardwalk Empire as Gillian Darmody, a showgirl at the Beaux Arts and mother to gangster Jimmy Darmody (played by Michael Pitt). She plays Sam Henessy, Attorney at Law, on the Netflix series Seven Seconds, February 2018.