Caltrain said the area around the station would be shut down for two to three hours and that trains are being allowed to proceed through the station at reduced speed.
Witnesses told ABC7 News that a group of people ran off after the shooting.
San Mateo Police Capt. David Norris said the man was shot in the abdomen and that his injuries are non-life threatening. The shooting was likely gang related, he added.
The shooting happened in the Caltrain parking lot, in a back alley behind businesses that's out of sight, Norris said.
Any witnesses should call the San Mateo Police Department.