The teen was identified as Shaaliver Douse, The New York Times reported.
The fledgling officer and a second rookie on foot patrol in the Bronx responded to the sound of gunfire about 3 a.m. EDT, saw one person running down the middle of East 151st Street following by a second person with a gun who was ordered to stop. There was another shot and then one officer fired a single shot, striking the youth in the jaw, the Times said.
The 26-year-old officer who shot is white and his 27-year-old partner is black, as was Shaaliver, the newspaper said.
Police officials said it appeared the officers followed department policies regarding use of deadly force.
Shaaliver was suspected of being a member of a youth gang called the Nine. Court records showed he had been found in possession of a gun at least once before, the newspaper said.
The boy's aunt, Quwana Barcene, 35, lamented the violence that plagues some NYC neighborhoods and compared her nephew to Trayvon Martin in Florida.
"Him, Trayvon Martin, it's never going to end," she said. "A child. Fourteen years old. Fourteen years old. Gone. Shot in the head. By police."
Commissioner Raymond W. Kelly offered condolences to the boy's mother, the Times said.
"Regardless of the circumstances, this is a crushing blow to any parent," he said.
New York's top cop added two videos reveal the shooting was justifiable. Kelly said one showed Shaaliver could be seen approaching several men, including one Kelly said was the target.
Shaaliver can be seen raising a gun and firing three shots, sending the group fleeing. A second video showed the target running around the corner in the street, a bullet flying past him and hitting a wall on the far side, producing a puff of smoke. Kelly said after the teenager was ordered to drop his gun, he fired again, though it was unclear whether he was aiming at the fleeing man or the officers.
"I think they did what we would expect officers of any experience level to do," Kelly said.