Born in Lake Charles, Louisiana and raised in Sugar Land, Texas, Flanery attended University of St Thomas in Houston where he took a drama class because of a girl. The girl was a short infatuation, but he found true love in college theater.
He moved to Los Angeles and waited tables. He got an agent and after eight months, began acting in television commercials and then other roles. He appear in two of the multi-part movies on Disney's Mickey Mouse Club: Just Perfect (1990) (TV) and My Life as a Babysitter (1990) (TV).
Early movie roles included Guinevere (1994) (TV), Frank & Jesse (1994), Powder (1995), Eden (1996), The Grass Harp (1995), and The Method (1997). One of his best known roles was probably on "The Young Indiana Jones Chronicles" (1992).