The 12:54 a.m. train from Huntington due in Port Jefferson at 1:41 a.m. hit the victim, described only as a man in his 40s, just east of the Northport station after 1 a.m.
“It is unclear what he was doing on the tracks,” an LIRR spokesman said.
Service was suspended on the Port Jefferson branch and passengers were held on the train for about two hours until another train arrived to continue on to the destination. Service was back to normal by the morning commute.
MTA police are continuing the investigation.