The entire line was suspended for hours due to police activity following the incident.
NJ Transit spokesman William Smith says the train was headed for New York City when it hit the man west of the Hazlet Station just before 4:30 a.m. Tuesday.
The 25 passengers aboard the train were taken by bus to the Matawan-Aberdeen Station and placed on another train.
Service resumed just before 8:30 a.m. with trains subject to 10 to 15 minute delays in both directions.
Some trains were canceled. Visit NJTransit.com for the latest on individual trains.