Police say the victims were killed while on the bridge that travels over Route 46 at around 9:45 p.m. They were pronounced dead at the scene.
A third teen, a 15-year-old from Little Falls, was taken to St. Joseph's Hospital with non life-threatening injuries sustained in the incident.
Route 23 north and Route 46 east were closed in the area during the investigation.
The survivor told first responders that the teens were walking on the tracks when they saw the train coming and ran, but that two of them didn't make it off the bridge in time.
Police have not said why they were on the tracks or where they were headed.