The lockdown went into effect at about 11:15 a.m. because of unconfirmed reports that the runaway teen was in the Albany area, Superintendent Marla Stephenson said.
The lockdown was lifted at about 1 p.m., Stephenson said.
The teen, a 16-year-old boy, was reported missing by his father this morning at about 1:15 a.m.
A handgun and ammunition were taken from his home at the time he ran away, Albany police spokeswoman Karina Tindol said.
The lockdown was a precautionary measure and was carried out at the request of police, Stephenson said.
"There was no direct threat to students, staff or a school," Stephenson said.
The missing teen, a student at MacGregor High School, a continuation school, was last seen at his home in El Sobrante wearing a black hooded sweatshirt, blue jeans and black tennis shoes.
He is white, 5 feet 5 inches tall and weighs about 130 pounds. Anyone who may have seen the boy is asked to contact Albany police at (510) 525-7300.