He was born in Daly City, California, the son of actors who divorced when he was five years old. He was raised by his father, Pete Rockwell, in San Francisco, while his mother, Penny Hess, stayed behind in New York (he spent his summer vacations with her). Rockwell had what The New York Times described in 1998 as a "footloose upbringing" and, at age 10, made his brief stage debut playing Humphrey Bogart in an East Village improv comedy sketch starring his mother. His mother had an unconventional lifestyle - she was involved with hippies, sex, and drugs.
He attended San Francisco School of the Arts with Margaret Cho and dropped out before graduation. He later received his high school diploma after his parents enrolled him in an Outward Bound-style alternative high school called Urban Pioneers because, as Rockwell explained, "I just wanted to get stoned, flirt with girls, go to parties." The school, the actor said, "had a reputation as a place stoners went because it was easy to graduate," but the program ended up helping him regain an interest in performing. After appearing in an independent film during his senior year, he graduated and moved to New York to pursue an acting career.
After his first film role in the 1989 horror film Clownhouse (produced by Francis Ford Coppola's production company) which he filmed when based in San Francisco, he moved to New York and trained at the William Esper Studios. His career slowly gathered momentum in the early 1990s, when he alternated between small-screen guest spots in TV shows like The Equalizer, NYPD Blue and Law & Order and small roles in films such as Last Exit to Brooklyn and Teenage Mutant Ninja Turtles. He also appeared as the title character in The Search for One-eye Jimmy. During this time Rockwell worked in restaurants as a busboy and delivered burritos by bicycle. At one point, Rockwell even worked as a private detective's assistant. "I tailed a chick who was having an affair and took pictures of her at this motel", he told Rolling Stone in 2002. "It was pretty sleazy." A well-paying Miller commercial in 1994 finally allowed him to pursue acting full-time.
The turning point in Rockwell's career was Tom DiCillo's 1996 film Box of Moon Light, in which he played an eccentric man-child who dresses like Davy Crockett and lives in an isolated mobile home. The ensuing acclaim put him front and center with casting agents and new-found fans alike, with Rockwell himself acknowledging that "That film was definitely a turning point....I was sort of put on some independent film map after 10 years in New York."
He also won strong reviews for the 1997 film Lawn Dogs, where he played a working-class lawn mower who befriends a wealthy 10-year-old girl (Mischa Barton) in an upper-class gated community in Kentucky; Rockwell's performance won him Best Actor honors at both the Montreal World Film Festival and the Catalonian International Film Festival. In 1999, Rockwell played prisoner William "Wild Bill" Wharton in the Stephen King prison drama The Green Mile. At the time of the film's shooting, Rockwell explained why he was attracted to playing such unlikeable characters. He said, "I like that dark stuff. I think heroes should be flawed. There's a bit of self-loathing in there, and a bit of anger... But after this, I've really got to play some lawyers, or a British aristocrat, or they'll put a label on me."