The fire broke out at about 8 p.m. under the Portal Bridge in Kearny which runs over the Hackensack River, an Amtrak spokesperson said.
Delays on New Jersey Transit trains were at least an hour.
The fire was extinguished but train service in and out of Penn Station was still delayed up to 45 minutes late into the evening.
Adding to the problems for NJ Transit riders was a disabled tractor trailer that was stuck on the tracks near Denville.
NJ Transit says service should be back to normal for the morning commute.
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