The boy, from Sayreville, New Jersey, was on a double-decker bus with about 65 other teenagers headed to New Jersey for a sweet sixteen party, according to Port Authority spokesman Al Della Fave.
They boarded the bus in Queens and crossed over the George Washington Bridge to New Jersey shortly after 6:30 p.m. ET on Friday.
As the bus exited the upper level to head toward Interstate 95, the boy opened the top hatch of the bus and stuck his head out, Della Fave said. His head struck the underside of the Fletcher Avenue overpass, causing extreme trauma.
The boy was rushed to Hackensack University Medical Center, where he was pronounced dead, police said.
No other physical injuries were reported, but the other teens on board the bus appeared to suffer severe emotional trauma. They were taken to a bridge administration building on a lower lot, where their parents picked them up, NBC New York reported.
Della Fave said two adults on were on board the bus at the time: the driver and an assistant. The assistant's role was not immediately clear.
Designer Transportation, which operates the bus, expressed its "deepest heartfelt sympathy" for the boy's family.
Police are continuing to investigate.
The accident caused long delays Friday night as the express lanes of the I-95 southbound from the bridge were shut down while emergency responders rushed to the scene and police investigated.
NBC New York and The Associated Press contributed to this report.
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