During the summer following his high school graduation, Bowen acquired an agent in New York City, then moved to Los Angeles. His first film role was as Kathryn Erbe's love interest in the comedy film What About Bob? (1991). He received a letter from Director Frank Oz before the film's release informing him that his role had ended up on the cutting room floor. Over the next few years, Bowen worked in part-time jobs, such as commercials and small roles in television, while also taking part-time screenwriting courses at the University of Southern California.

In 1995, Bowen was hired to play the lead role in Fox Hunt, a live-action interactive video game from Capcom. His character, Jack Fremont, is a comedic twist on a "James Bond" type of character. Fox Hunt was later developed as a potential television series. Bowen's performance in the game was also noticed by executives at Warner Bros., who signed him to a talent development deal.

While Bowen raised the money he needed to finish his film, he continued acting, landing recurring roles on ER and Reno 911! as well as guest roles on programs such as CSI: NY, Las Vegas, JAG, Charmed. He also appeared in movies such as Ivan Reitman's Evolution (2001) and starred in several television pilots, including Breadwinners for producers Gale Anne Hurd and Steven Tao. In addition, Bowen has lent his voice to the video games Ice Age: The Meltdown, Rise of Nations, Yakuza, The Matrix: Path of Neo, Mortal Kombat X and others.

Bowen eventually filmed the pilot for Fox Hunt, but the show was not picked up. Instead, he joined the cast of Fox's MADtv later that year and was quickly called one of the new talents to watch by TV Guide. Despite his success, Bowen left the show after one season, and with the help of his father he raised enough money to start principal photography for Along the Way (aka The Haven]. He gained over 40 pounds in order to play the hulking character "Jocko" in the film. Scott Weinberg wrote, "Andrew Bowen (formerly of the underrated MADtv) is stunningly strong as Jocko, creating a character that on the surface seems like little more than an affable giant, yet the actor brings a fierce sense of loyalty, a goofy sense of humor, and an overall air of desperate sadness to this role. He delivers easily one of the best 'unknown' performances I’ve seen in years."