Trains departing just after 9 a.m. from stations in San Jose and San Francisco were on time and regular service was expected to resume for the remainder of the day, Caltrain spokeswoman Christine Dunn said.
At about 5:35 a.m., northbound train No. 103 struck and killed a man at the Charleston Avenue crossing, Dunn said.
A preliminary investigation indicated that the incident was a suicide, Dunn said.
No injuries were reported among the 55 passengers aboard the train who were later transferred to another train at East Meadow Drive.
Trains were single-tracked through Palo Alto at around 10 mph until 8:40 a.m., causing system-wide delays of up to an hour and a half during the morning commute, Dunn said.
The Santa Clara County medical examiner's office was working to identify the victim and make a final determination regarding the cause of death, a deputy said.
The fatality is the 11th on the Caltrain right of way so far in 2012, five of which have been determined to be suicides, Dunn said.
There were 16 Caltrain-related fatalities in 2011.
