The boy was crossing Alameda De Las Pulgas at Aragon Boulevard in a crosswalk when he was hit at about 7:45 a.m.
Witnesses told police the light for northbound and southbound Alameda De Las Pulgas had just turned green when the accident happened, San Mateo police Lt. Mike Brunicardi said.
The teen was taken to a local trauma center where he remained hospitalized this afternoon. Brunicardi said his injuries were not life-threatening.
The driver, a 35-year-old San Mateo woman, has not been cited or arrested, Brunicardi said. It appears she had the right-of-way and that the boy "had dashed to get to school and subsequently ran into the side of the car," he said.
The crash remains under investigation.
Authorities are reminding drivers and pedestrians to be cautious around intersections, particularly in school zones.
On Wednesday morning, two 13-year-old Pleasant Hill Middle School students were seriously injured when a car hit them as they crossed a street in a crosswalk near the school. Police said the driver may have been blinded by the sun.