In 1989, Perrineau was cast as the original Tyrone Jackson in the world premiere of the stage adaptation of the 1980 hit movie Fame (now known as Fame: The Musical) at the Walnut Street Theatre, in Philadelphia, Pennsylvania. Perrineau took the role of Link in The Matrix series after the original operator Tank was written off the script when Marcus Chong was fired over monetary disputes. Lost co-star Adewale Akinnuoye-Agbaje starred with Perrineau on the HBO series Oz.
Perrineau played the character Michael Dawson on ABC's hit show Lost. He was temporarily written off when his character left the island with his son at the end of season two and did not appear at all in season three. In July 2007, it was announced Perrineau would return to the main cast for the show's fourth season. However, this return was short lived, as the fourth season was his last as a regular cast member. He made one guest appearance in the sixth and final season.
Perrineau appeared in the 2008 music video, "Yes We Can".
Since his debut single "Stay Strong" in 2007 Perrineau has been working on his musical career. He is actively collaborating with music Producer Tomo in der Muhlen, known as DJ Tomo Tom Tom, on his debut album, Seeker. The first single, "Moving On," was released October 15, 2011. Having his creative roots on the stage, Perrineau enjoys doing live shows where he performs with a full band: two guitars, bass, drums and keyboards. He performed at Los Angeles club The Mint in April 2010. Perrineau has appeared in the MKTO - Thank You Music Video and J. Cole's - She Knows music video.
Perrineau starred as Stevie, the bass player, in the TBS comedy Wedding Band, which ran from 2012 to 2013.
Perrineau starred as Manny, an Angelic messenger, in Constantine, the short-lived 2015 television series based on the DC Comics/Vertigo character John Constantine.
He makes his Broadway debut in the Roundabout Theatre Company production of The Cherry Orchard by Anton Chekov and adapted by Stephen Karam. The play runs from September 2016 to December 4, 2016. Perrineau plays the role of Lopakhin with Diane Lane as Ranevskaya. Also in 2016, Perrineau co-starred in the Amazon Studios legal series Goliath.