At age 13, Sean Astin debuted on the silver screen as Mikey in The Goonies (1985). He had a small role in 1989's The War of the Roses and in 1993 got a memorable part as the title character in Rudy. Astin played Samwise Gamgee in Peter Jackson's The Lord of the Rings film trilogy. He also played the brother of Lucy (Drew Barrymore) in the Adam Sandler film, 50 First Dates. He provided the voice for Balto's son, Kodi, in the second direct-to-video sequel of Balto.

In 1994, he directed and co-produced (with his wife, Christine) the Academy Award-nominated short film, Kangaroo Court.

In 1995, he starred in the Showtime sci-fi film, Harrison Bergeron, an adaptation of the short story by Kurt Vonnegut. In this futuristic film, the world focuses on the belief that "All men are not created equal. It is the purpose of the Government to make them so." The titular character, Harrison, is smarter than his peers and is unaffected by the standard technology used to handicap all Americans so that everyone is of equal ability.

While working on The Two Towers, he persuaded a number of fellow cast and crew members, including director Peter Jackson, to act in or work as crew on his short film, The Long and Short of It (2003), which takes place on a street in Wellington, New Zealand. The film premiered at the Sundance Film Festival, 2003, and appears on the "standard edition" DVD of The Two Towers as an extra feature together with a "making of" video.

Astin appeared as Lynn McGill in the fifth season of the FOX drama 24. He also appeared in the first season of the NBC Show, Las Vegas, as a gambler who wins one million dollars, and his wife and best friend want to take it away from him. He also had a role in Adam Sandler's 2006 film, Click. Astin was the narrator of the U.S. version of Meerkat Manor, shown on the Discovery Channel-owned cable TV channel, Animal Planet. He most recently appeared as a sales clerk in an episode of the TV series, My Name Is Earl, in which he, along with co-stars Charles S. Dutton and Chelcie Ross, parodied their hit movie, Rudy. Scenes included a motivational speech by Dutton after Earl fails his chance at becoming a sales rep, and all the dock workers turning in their credit cards to Ross. Both of these are representations of famous "Rudy" scenes.