The 16-year-old surrendered to detectives on Friday.
He was arrested and charged on Friday with Murder and Criminal Possession of a Weapon, police said.
The development follows the NYPD's release of images of the suspect on Thursday.
Police said the person of interest is a 16-year-old boy who attends the nearby Campus Magnet High School.
Mayor Eric Adams had previously said that the motive was an ongoing gang dispute.
The family of 13-year-old Sanjay Samuel spoke outside Cohen's Children's Hospital on Wednesday, announcing that the teen had died.
Police say Samuel, a high school freshman, was in the Dunkin' parking lot with his friends on Monday morning when someone rolled up on the group on a scooter and immediately sparked an argument. A fight ensued, with the victim throwing punches at the person of interest, who allegedly pulled his weapon and fired a shot, hitting the 13-year-old in the head.
Surveillance video showed a boy running into a deli, appearing to tell other kids what happened. They come outside, stunned and upset.
Detectives also recovered surveillance video that indicates the shooting was targeted.
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