The man was struck by a northbound train at about 9:30 a.m. on the train tracks at Ravenswood Avenue, Caltrain spokeswoman Tasha Bartholomew said.
The victim's identity is not yet being released by the San Mateo County coroner's office.
The death prompted trains to use a single set of tracks through the area, causing delays of 30 to 40 minutes. All tracks reopened and trains were back on schedule as of 11:50 a.m., Bartholomew said.
The incident is Caltrain's fourth fatality of 2012. There were 16 fatalities on its right of way last year.
The agency released a statement about this morning's death.
"It is always regrettable when a life is lost. Caltrain reminds everyone to be safe around train tracks. Caltrain would also like to thank our passengers for their patience while we deal with these sad incidents," the statement said.
In an effort to reduce fatalities, in 1996 Caltrain installed no trespassing signs along its railroad. In 2001, signs with a crisis hotline number were also added. The signs are posted every 500 feet along the 55-mile length of the railroad, according to the agency.