Billie McGee left her house in the city's Ingleside neighborhood but never arrived at the S.R. Martin College Preparatory School, The San Francisco Chronicle reported Wednesday.
The seventh-grader is described as an African-American girl, 5-feet-5-inches tall, weighing 140 pounds.
At the time she disappeared, police were told she was wearing a school uniform that consisted of a black and white jacket with a white-colored shirt and black pants.
"Someone took her," said Tina Brown, Billie's mother.
Police Sgt. Steve Mannina said authorities were treating the disappearance as a missing person's case.
Anyone with information about the girl is asked to call the San Francisco Police Department's Missing Person Unit at 415-558-5508.