The shooting happened at about 6:20 p.m. Thursday on a bus in the Bedford-Stuyvesant neighborhood.
The boy was taken into custody and a firearm was recovered. No charges were immediately filed.
Police say 39-year-old Angel Rojas of Brooklyn was taken to Woodhull Hospital, where he was pronounced dead. They say he was not the intended target.
According to The New York Times, the shooting erupted during an argument among a group of teenagers. The newspaper reports that more than one shot was fired.
Relatives say Rojas came to the United States four years ago from the Dominican Republic with his wife and two children.