The agency says the accident occurred on the Brentwood-North Bay Shore border early Friday morning.
The accident involved the 5:29 a.m. train from Ronkonkoma, due in Penn Station at 6:38 a.m. The person was struck around 5:50 a.m.
The LIRR says it's not clear if the victim was trying to cross the tracks or if the gates were functioning properly.
The accident remains under investigation.
The 8:15AM from Penn, due Ronkonkoma 9:39AM, was the first train to operate east of Farmingdale. The 9:11AM from Ronkonkoma, due Penn 10:32AM was the first westbound.