It happened around 2:30 a.m. at 1943 Highway 24/87 - north of Spring Lake - which is between Raleigh and Fayetteville.
Harnett County Sheriff Larry Rollins told ABC11 Eyewitness News that two Harnett County sheriff's deputies approached who they thought was a suspicious looking man sitting in a ditch in front of a convenience store at that address.
Corporal S. Assman and Sgt. T. Dagett stopped and got out to ask the suspect what he was doing.
"When he saw the weapon, he turned to the suspect who pulled a 9mm pistol from his waistband and started firing," Rollins told ABC11.
Assman was hit in the leg. Deputies returned fire - killing the teen.
Rollins said when the deputies searched the suspect's bag; they found 250 rounds of ammunition and a gun. The sheriff said the teen also had two more guns on him.
The wounded deputy was rushed to Cape Fear Valley hospital where he was treated and released.
Rollins said his men did the right thing although at the time they had no idea the suspect was only 13-years-old.
"When you have the option to sit down and think about things and you know that it's a child it's like one of them said, 'why, why did he do it,'" Rollins said.
It's still unclear what the boy's intentions were.
Authorities are not releasing the teen's name because of his age, but Rollins told ABC11 the boy was an Overhills Middle School student from the Anderson Creek community. ABC11 was able to confirm through the medical examiner's office that the teen's name was Joe Wheeler.
Grief counselors were on hand at the school on Wednesday.
Rollins said the boy's parents did not know he was not at home before the incident.
He also said the North Carolina State Bureau of investigation was investigating - which is routine after any officer involved shooting.