Train 562 was en route from Los Angeles Union Station to San Diego when it struck the pedestrian at approximately 6:20 a.m., according to an Amtrak spokesperson.
There were 30 people aboard the train, including passengers and crew.
Orange County Line trains 601, 603, 605, 683 and 91 Line trains 701 and 703 were expected to face delays. Metrolink commuter trains were also delayed because of the investigation.
Amtrak trains 564 and 573 were canceled and Amtrak expected delays throughout the day.
The identity of the victim was not immediately released.