The investigation ended just after 11 p.m. No explosives were found.
Police said it began at 9:30 p.m. out of the train station in Simi Valley with a woman who was getting onboard.
Officials said a man who was with her made a comment to an Amtrak worker that raised concern.
It is unclear what the man said, but it related in some way to a bomb scare involving the woman and her bag.
Police said the train was evacuated and each passenger was checked by authorities.
The woman was cooperative, authorities said.