The incident was reported in a Lower Manhattan station around 5:30 p.m.
The boy was taken to the hospital where he was pronounced dead.
Police said his mother was holding bags while walking down the stairs, with the boy walking in front of her.
The child made it down to the bottom of the stairs and onto the train platform before her, then approached the oncoming train and was pinned between the platform and the train, police said.
NYC Transit President Andy Byford released the following statement:
"NYC Transit and NYPD are investigating a tragic incident at Fulton Street Station where a young boy apparently became separated from his mother and was struck by a northbound number 2 train at 5:36 p.m. The circumstances surrounding the incident remain under investigation. The boy was removed to a local hospital by EMS and was later pronounced deceased. Our hearts break for the family and the MTA is praying for them. Our thoughts are with the crew of the train as well."