It happened in the 800 block of Ninth Street just before 3 p.m. when a male dressed in all black and wearing a mask robbed the store at gunpoint.
Nearby E.K. Powe Elementary School was put on lockdown for a short time.
At last report, police were searching for the suspect who was believed to be a 16-year-old boy. They also think he may have had a getaway car driver.
The store clerk was not injured.
Anyone with information is asked to call CrimeStoppers at (919) 683-1200.