Train No. 198 left San Francisco station at 12:01 a.m. and hit the pedestrian on the tracks about 100 yards north of 25th Avenue at around 1 a.m.
There were 62 passengers on the train at the time of the incident, officials said.
The train was able to continue southbound shortly after 2 a.m. and made all scheduled stops.
The next train is scheduled to leave San Jose Diridon station at 4:30 a.m. and officials do not expect this incident to cause delays in the morning commute.
Emergency crews were on the scene as of 2 a.m. Further information about the incident was not immediately available.