Born in Lake Charles, Louisiana and raised in Sugar Land, Texas, Sean Patrick Flanery attended St. Thomas Houston University. At university, he took an acting class because he had a crush on a girl in the program. Although the crush turned out to be pure infatuation, he developed a love of acting. He moved to Los Angeles and worked as a waiter until he landed an agent.
It took him another eight months to land his first television commercial, but after that, things began moving fairly quickly. He played supporting roles in a couple of TV movies aimed at teens, then at age 26, landed the title role in the TV series The Young Indiana Jones, produced by George Lucas. The show only ran from 1992 to 1993, but he reprised the character for nine TV movies over the next seven years.
His first starring role in a feature was as the title character in Powder (1995), for which he was nominated for an MTV Movie Award. Flanery earned more recognition as Conner MacManus in The Boondock Saints (1999) and reprised the character in Boondock Saints II: All Saints Day (2009). He played a supporting role in the big budget film Saw 3D (2010).
In 2016, his first novel, Jane Two, was published.
Most recently, he played the starring role in the horror/thriller Nefarious (2023).
Sean's daughter Lola Flanery, whose mother is model Sasha Grierson, was born on May 26, 2005 and was raised in Toronto. He also has two children, Porter and Charlie, with his wife, actress/model Lauren Hill.