After graduation, Bowen had a role in the soap opera Loving and made her primetime debut on an episode of the college drama Class of '96. She also had the lead role in the 1994 television film Runaway Daughters, playing opposite Paul Rudd.

In films, Bowen played the love interest of the title character in Happy Gilmore. Roles in other films include An American Werewolf in Paris and Multiplicity. On television, she has had guest roles on Party of Five, Strange Luck, and a recurring role on ER as the girlfriend of Dr. Carter. On the sketch comedy program Stella Shorts, Bowen played an angel in the "Raking Leaves" episode.

Perhaps Bowen's best-known role was on the television series Ed, where she played high school English teacher Carol Vessey and the love interest of the protagonist, Ed Stevens. Since then, Bowen guest starred as the character of Sarah Shephard in five episodes of Lost. In the fall of 2005, Bowen joined the cast of Boston Legal, playing attorney Denise Bau