Hercules police spokeswoman Detective Connie Van Putten says detectives interviewed the student Tuesday and determined nothing had happened to him.
On Monday, the 15-year-old student reported he was attacked by three boys in a bathroom at a suburban San Francisco public school.
The teen, who is biologically female but identifies as male, had told officers he was leaving a boy's bathroom late Monday morning at Hercules Middle/High School when the assailants pushed him inside a large stall and attacked him.