In spring 1989, Flockhart made her first television appearance in a minor role in an episode of Guiding Light as a babysitter. She made her professional debut on the New York stage, appearing in Beside Herself alongside Melissa Joan Hart at the Circle Repertory Theatre. Two years later, Flockhart appeared in the television movie Darrow. Though she later appeared in films Naked in New York (1993) and Getting In (1994), her first substantial speaking part in a film was in Quiz Show, directed by Robert Redford.

Flockhart debuted on Broadway in 1994, as Laura in The Glass Menagerie. Actor Julie Harris felt Flockhart should be hired without further auditions, claiming that she seemed ideal for the part. Flockhart received a Clarence Derwent Award for her performance. In 1995, Flockhart became acquainted with actors such as Dianne Wiest and Faye Dunaway when she appeared in the movie Drunks. Later that year, Flockhart starred in Jane Doe as a drug addict. In 1996, Flockhart appeared