Southbound train No. 422 was traveling from San Francisco when the conductor reported seeing something in one of the train tunnels at about 8:25 a.m., Caltrain spokeswoman Christine Dunn said.
The train stopped at Bayshore Station in Brisbane and transit police responded to the report.
A man was found trespassing in the tunnel, Dunn said.
The man, who was not injured, was arrested.
The train departed Bayshore Station at 9:20 a.m., about 50 minutes behind schedule. There were no further Caltrain delays this morning, Dunn said.