Perrineau was born in Brooklyn, New York, the son of Harold Williams and Sylvia Perrineau. His parents changed his name to Williams when he was seven. Harold later legally changed his name back to his birth name, after discovering there was already a Harold Williams in the Screen Actors Guild union. Perrineau attended Shenandoah University, but did not graduate. Perrineau and his wife, Brittany, have three daughters, Aurora Perrineau, born 1994, Wynter Aria, born on May 7, 2008, and Holiday Grace, born on March 21, 2013. Brittany had recurring appearances on US TV show Lost, appearing in the Season 1 episodes of "Outlaws", as the girlfriend of Sawyer, and in the episode "Numbers", as the woman who read the lottery numbers. Her acting credits also include the role of Dara in the romantic-comedy Saving Face, as well as appearing in Your Name Here.
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.
He stars also in 30 Days of Night: Dark Days along with Rhys Coiro, Mia Kirshner, Kiele Sanchez (also a Lost co-star), Diora Baird and Monique Ganderton.
Perrineau appeared in the 2008 music video, "Yes We Can".
Perrineau voiced the title character from Marvel's Blade anime series on G4 January 2012. He was cast to play the character of Damon Pope the main antagonist of Season 5 of the hit show Sons of Anarchy.
Perrineau starred as Stevie, the bass player, in the TBS comedy Wedding Band, which ran from 2012 to 2013.
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
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 Tom Tom, on his soon-to-be-released 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.