NJ Transit spokesman Dan Stessel said rail equipment was being moved when a person came off the station platform and was struck.
Trains were leaving Penn Station on time, but they would only get as far south as Rahway before hitting delays.
Eastbound trains were bypassing New Brunswick, Edison and Metuchen.
Delays continued until around 7:00 p.m. as police investigated.
The person struck by the train was not immediately identified.