The boy, whose name was not released, was accused of robbing the store in the 1000 block of Petit Avenue in Ventura about 1:30 a.m.
The suspect entered the store, showed the clerk a handgun and demanded money before fleeing from the store, according to the Ventura Police Department.
Officers responding to the call began searching the area and found a suspect who matched the description given to them.
The boy was charged with robbery, possession of stolen property and committing a felony with a loaded gun. He was booked at juvenile hall.
No one was injured.