Noxon was born in Los Angeles, California, to National Geographic documentary filmmaker father, Nicolas Noxon, and Mary Straley. Noxon has said that she grew up in nearby Santa Monica, and that her mother was gay. She has a brother, Christopher Noxon, who is a writer and is married to TV writer Jenji Kohan. Her grandmother was painter Betty Lane. Noxon would often accompany her father when he traveled to shoot documentary films and was already in love with the idea of movies.
Noxon graduated from Oakes College at the University of California, Santa Cruz in 1987 with a B.A. in Theater Arts.