In 1995, Flynn earned a nomination for Primetime Emmy Award for Outstanding Guest Actress in a Drama Series for her performance on ER. She starred on short-lived series such as Flipper and To Have & to Hold. She also appeared in a recurring roles on China Beach, The Practice, Judging Amy and Nip/Tuck. Flynn guest-starred on television series such as The X-Files, Crossing Jordan, Without a Trace, The Drew Carey Show, Everwood, The Closer, Cold Case, House and Grey's Anatomy. Her film credits include Last Exit to Brooklyn, Serving in Silence: The Margarethe Cammermeyer Story, Two Mothers for Zachary, Clear and Present Danger, Pay It Forward and Project X.