Train No. 319, a Baby Bullet express train, was taken out of service. Another express train was scheduled to depart the San Jose Diridon station at 7:45 a.m.
Two other northbound trains, No. 221 and 223, are up to 25 minutes behind schedule, Caltrain spokeswoman Christine Dunn said.
Baby Bullet train No. 323 is about five minutes late.