The campus, located at 177 N. San Pedro Road near the Marin County Civic Center, was evacuated after the sheriff's office was notified around 7:45 a.m. about the threatening message, which was left overnight, sheriff's Lt. Keith Boyd said.
Students and staff were directed to the San Rafael National Guard Armory at 153 Madison Ave., where there is food and water available, as well as teaching materials.
Boyd said school officials are asking parents to not pick up students at the school or the evacuation site.
As of 9:45 a.m., a bomb squad was searching the campus for any suspicious devices, Boyd said.
The California Highway Patrol, San Rafael Police Department and school personnel are assisting.
The sheriff's office is investigating who is responsible for the threat, which was isolated to the school. Nearby businesses, homes and other buildings have not been affected, according to Boyd.
