The Metropolitan Police Department said the shooting happened around 3:56 a.m. in the 1000 block of Quincy Street, not far from Brookland Middle School and Turkey Thicket Recreation Center.
According to investigators, the unidentified person confronted and shot the 13-year-old after claiming that the boy was breaking into several vehicles along the street.
They said the boy was shot multiple times.
There is no indication of who placed the 911 call reporting the incident.
Police did not release specific details about the confrontation, but add that there was no indication that the 13-year-old was armed.
The 13-year-old was identified by police as Karon Blake, of Northeast D.C. Police confirmed to FOX 5 that Blake was a student at Brookland Middle School.
Investigators said, when officers arrived at the scene, they found the person performing CPR on the boy.
The 13-year-old was taken to an area hospital after the shooting, and later pronounced dead.
Investigators said that the firearm used in the shooting was legally registered, and the person is cooperating with authorities.
While investigating the incident, police found a car on Quincy Street that had been previously reported stolen, and is believed to have been used by the 13-year-old.
Investigators believe two other juveniles were also involved in the incident.
According to a neighbor in the area, the two tried fleeing the scene in a vehicle, before bailing out in an alley and running away on foot.
Authorities are still working to determine whether any criminal charges are warranted against the person.
Anyone with information on the shooting is asked to call MPD at 202-727-9099 or send a text tip to 50411.
This is a developing story. Stay with FOX 5 for updates.