Trains, however, will continue to run behind schedule throughout the afternoon, Caltrain spokeswoman Christine Dunn said.
Caltrain will apologize to commuters for the inconvenience by offering free rides for the rest of the day, Dunn said. The free rides will end at 1:30 a.m. Friday.
The computer glitch also affected Amtrak, causing one- to two-hour delays on trains 527 and 528, which run through Fremont on routes between San Jose and Sacramento, Amtrak spokeswoman Vernae Graham said.
Amtrak set up bus bridges and taxi service between Fremont and Great America Parkway to bypass the area affected by the signal problems, Graham said.
The Santa Clara Valley Transportation Authority will accept all Caltrain fares on El Camino Real bus routes, Caltrain spokeswoman Christine Dunn said. Samtrans will accept Caltrain fares on its buses for the rest of the day.
The signal problem began around 9 a.m. and the computer system was repaired by about 12:45 p.m.