Southbound train No. 102 struck the pedestrian at about 5:20 a.m. on the tracks between South Linden Avenue and Scott Street, about a mile north of the San Bruno Caltrain station, spokeswoman Christine Dunn said.
Dunn said the circumstances of the death remain under investigation.
The incident caused Caltrain delays in both directions.
Service was fully restored at about 7 a.m., but trains were running at a reduced speed of 30 mph, Dunn said. Trains have since gotten back on schedule.
During the closure, southbound Caltrain riders were advised to take BART as far as the Millbrae station and transfer to Caltrain for the remainder of their commute, Dunn said.