Flanagan was born in Bryn Mawr, Pennsylvania. In 1990, he starred in the short-lived ABC police drama Sunset Beat.
He co-starred in the Nickelodeon series Unfabulous as Jeff Singer, the father of Emma Roberts' character, from 2004 to 2007. His other television credits include CSI: Crime Scene Investigation, CSI: Miami, Judging Amy, and Northern Exposure. Flanagan also played one of Phoebe's many boyfriends in the television sitcom Friends in the third season. He also had a recurring role as Harry Dean on Fox's Melrose Place. Flanagan studied with Sanford Meisner in the last class taught by Mr. Meisner at Neighborhood Playhouse Acting School in New York City.
