The shooting happened at about 6:20 pm yesterday 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 pronounced dead at the hospital. 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.