The person was struck by southbound train No. 210 just south of the Hayward Park station at about 7:20 a.m., Caltrain spokeswoman Christine Dunn said.
He was hit in an area where there is no designated crossing. "There was no reason for the person to be on the tracks," Dunn said.
The 350 passengers aboard that train were taken to the Hillsdale station, according to Dunn.
Trains that were halted while investigators were on the tracks began running again after the tracks reopened around 8:40 a.m., Dunn said.
Northbound and southbound trains continued to face delays at 11 a.m. of about 10 to 30 minutes, and were traveling at a reduced speed through the area of the fatal collision, Dunn said.
All trains were expected to be running on time and at full speed by noon.