The train stopped at the Orinda station when smoke was reported on the train shortly after 6 p.m. on Wednesday, BART spokeswoman Alicia Trost said.
Trost said firefighters arrived at the station at about 6:20 p.m. and that the smoke was found to be coming from beneath the train.
Passengers were evacuated and the train went out of service, BART police Lt. Tyrone Forte said.
The train remained on the tracks at the Orinda station until after 6 a.m. as crews worked to cut through a 1,600-pound metal motor reactor, which had to be removed from the tracks before the train could be moved. The disabled train has been moved to a yard for repairs.
According to a BART spokesperson, the incident is not related to a reenactment held Wednesday of an accident that killed two workers on the tracks Saturday.