Flanagan was born in Bryn Mawr, Pennsylvania. He co-starred in the Nickelodeon series Unfabulous as Jeff Singer, the father of Emma Roberts' character, from 2004 to 2007. 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 made his major acting debut opposite Matthew Broderick and Christopher Walken in the 1988 film Biloxi Blues based on the Neil Simon play. He was also in Holiday in the Sun with the Olsen twins, playing their father.
Flanagan has written five plays and is the founder of the L.A. Café Plays series in Santa Monica. He is also the author of One Less Bitter Actor (Sentient Publications, 2008, ISBN 978-1-59181-063-6), a guide for those trying to make it in show business.