NJ Transit spokeswoman Penny Bassett Hackett says the three were on a railroad bridge over Route 46 in Wayne when the train came down the tracks at 9:45 p.m. Sunday.
Bassett Hackett says one of the boys managed to jump down an embankment. He was taken to St. Joseph's Hospital in Paterson. The extent of his injuries is not known.
The train was headed to a maintenance yard in Kearny and was not carrying passengers.
Bassett Hackett says NJ Transit police are trying to determine why the boys were on the tracks.
Their names, hometowns and ages have not yet been released.