Hannigan was born in Washington, D.C. She is the only child of Emilie Posner Haas, a real estate agent, and Al Hannigan, a truck driver. Her father is of Irish descent and her mother is Jewish.Her parents divorced when she was two and she was raised mostly by her mother in Atlanta, Georgia.
At age four, Hannigan began appearing in commercials. She moved to Hollywood at age 11. Living with her mother and attending North Hollywood High School, she successfully auditioned for agents while visiting her father in Santa Barbara. After attending North Hollywood High School, she attended California State University, Northridge where she earned a degree in psychology.