The newest incident happened at 7:48 p.m., when a southbound train "struck a person who was trespassing on the tracks near the Castro Street crossing in Mountain View," Caltrain said in a news release.
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All trains are stopped in the area to allow emergency personnel to investigate the scene.
There were no reports of injuries to about 118 passengers on the train.
In the earlier fatality, a person was struck by a northbound train in Burlingame at 4:45 p.m., Caltrain reported. No passengers reported injuries.
The two incidents are the eighth and ninth fatal strikes this year.