The incident happened just before 8:30 a.m. and caused significant delays up to an hour in and out of Penn Station.
NJ Transit said the victim was trespassing when they were hit by the train.
The agency President and CEO Kris Kolluri helped passengers board a rescue train into Newark Penn Station after the incident.
"We sincerely apologize for this morning. As we told you this morning there was a trespasser strike. Now that you're all safely in the car we look forward to getting to the destination," said Kolluri.
NJ Transit said tickets will be cross-honored by PATH at Hoboken, Newark Penn Station and 33rd Street-New York.
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