Sean was born in Westchester, New York, on April 16, 1975 to Joseph and Margaret Maher. He has an oldersister and a younger brother.He became interested in acting after performing in a play at summer camp. Sean graduated from New York University with a Bachelor of Fine Arts in Drama.
Sean's first television series was the Fox series entitled Ryan Caulfield: Year One. It was canceled after the first two episodes. Despite the failure of the show, Sean received favorable reviews and was cast in a recurring role on Party of Five in 2000 as Julia Salinger's love interest. After his work on Party of Five, Sean co-starred in The $treet as an ex Nay Seal turned Wall Street trader. The show was not successful. In 2001, he starred in the ABC/Disney remake of Brian's Song.
In 2002, Sean accepted the role of Simon Tam on the Joss Whedon series, Firefly. The series was canceled after only 11 of 13 episodes were aired.
Sean made his feature film debut in 2004 starring in the independent film, Living 'Til the End. In 2005, he reprised the role of Simon Tam in the Joss Whedon's film, Serenity.
Maher came out in 2011, using his role as a closeted gay man in a sham of a marriage in The PlayboyClub as a platform. He is in acommitted relationship with his partner Paul, withwhom he has two adopted children, Sophia Rose and Liam Xavier. After Sophia was born, he took two years off from acting to be a stay at home father.