Caltrain officials received a phone call around 2:45 p.m. Monday saying there was a bomb aboard one of the trains. All of the San Francisco trains were searched and no device was found.
Service was suspended between Millbrae and San Francisco as police continue to search additional trains.
Riders have been advised to use BART to get between Millbrae and San Francisco; BART is honoring Caltrain tickets.
Twitter users have been posting new information about the service delays.
Service was restored at 5:20 p.m., according to Caltrain spokesperson Christine Dunn.