It happened around 8:15 a.m. Thursday at the Chestnut Street crossing.
The victim was a Palmyra High School student-athlete, but his name has not been released.
"He was academically a great student, well-liked by all his friends. All his brothers have that energy that people just kind of draw to," said Interim Superintendent Mark Pease.
Pease says the rising sophomore was fatally struck as he crossed the tracks to get to soccer practice.
Grief counselors will be at the school Friday (8 a.m. to 4 p.m.) and Saturday (8 a.m. to 2 p.m.) to assist the community during this difficult time.
"It was sad, very sad. A tremendous amount of emotion and the impact on these young people. It's going to live with them for the rest of their lives," said Pease.
The area where this incident happened is an area students often cross, according to Pease. In fact, he told Action News the district brings in New Jersey Transit every year to conduct safety lessons for the students about how to properly cross the tracks.
Mayor Gina Tait says there will be a further discussion with NJ Transit to ensure the area is safe.
"When school is in, over the crossing, we have a crossing guard. There is an area though that has an opening in the gate that we will have to see what New Jersey Transit will do," said Tait.
In the meantime, this small community is grieving this loss and vowing to do whatever it can to help those affected.
"It's going to have a huge impact, that's the scary thing about it. We don't know how long of an impact it will have on this community," said Pease.
A total of 29 people were on board the train at the time of the incident. There were no injuries to any of the passengers.
Further details on the circumstances surrounding this incident have not been released.