Templeton Middle and Elementary Schools sheltered in place after middle school staff received word about a threat on Monday morning.
Staff said the threat was general and not specific.
Officials told students and staff at the middle school, located at 925 Old County Rd., to shelter in place at 10:50 a.m.
Nearby Templeton Elementary School was also told to shelter in place out of an abundance of caution, officials said.
Classes and activities continued while many San Luis Obispo County Sheriff's Office personnel searched the school.
The Shelter in Place was lifted at about 1 p.m., though authorities say they will stay at the school through the day.
The threat is still under investigation.