It happened just after 4:30 a.m.
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The MTA said the "unauthorized person" was struck east of the Woodside station.
There was no immediate word on the victim's identity or how that person ended up on the tracks.
LIRR service was temporarily suspended westbound between Jamaica and Penn Station.
Eyewitness News is told service was restored within an hour, but commuters were advised to "anticipate delays, cancellations and diversions."
Delays of about 20 minutes were still being reported at 8 a.m.
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By 10 a.m. most trains were back operating on or close to schedule, with a few residual delays reported.
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