The Fire Department said that one vehicle of the train had derailed and three people had been injured. The city's Fire Department said there was smoke but no fire.
Passengers told CBS New York they felt the train jump around 125th Street.
The Fire Department of NY said a handful of people were treated for minor injuries at around 10 a.m.
The chairman of New York's Metropolitan Transportation Authority says transit officials are investigating why the train's emergency brakes went on before the derailment approaching the station at 125th Street and St. Nicholas Avenue.
Some passengers reported the lights and air conditioning failing on their carriages after several trains along lines B, C, A D were affected by the stoppage.
An Eyewitness News viewer captured this photo showing the situation on D train that was headed toward 125th Street: One passenger posted on social media about her ordeal: This is a breaking news story. The outage happened at 9:48 a.m. and is causing trains to hold at the station.
"One lady began having a panic attack, and most people had to use their shirts to not breathe in the smoke (from the accident)". He said the station wasn't smoky, but there was a strong, acrid smell. A report earlier this month found rush-hour cancellations and delays on New York's Long Island Rail Road are at the highest level in 10 years.