Nicole Houston Reed was born in West Los Angeles, California, to Cheryl Houston, a beautician, and to Seth Reed, a production designer. She has an older brother, Nathan August Reed, and a younger half-brother, Joey Reed. Her mother is a Christian of mostly English descent as well as Irish, Scottish, German and some Italian whereas her father is Jewish. Reed was raised without religion and has identified as Jewish. She grew up around some Jewish practices, as her brother had a Bar Mitzvah.
Reed has said in numerous interviews that her early home life was "complicated". Her parents divorced when Reed was two, after her mother found her father in bed with another man. She was raised by her mother. In 2002, when Reed was 14 years old, she moved out of her mother's house and began living on her own, mainly in apartments in the Los Angeles area. After Thirteens success, Reed returned to Alexander Hamilton High School in Los Angeles, but dropped out again after a year. She said that "mothers who were sneaking into the school at lunchtime to confront and harass her about the film" were the reason for her departure. She earned a high school diploma through homeschooling.