Nathanson was born on October 12, 1965, in Los Angeles County, California. He attended the University of California, Santa Barbara as an English major from 1983 to 1985. While at UC Santa Barbara, he worked on the school's newspaper, the Daily Nexus, and has stated that the courses he took at UC Santa Barbara led him to wanting to become a screenwriter. He later enrolled in the screenwriting program at the AFI Conservatory for one year.