It happened around 1:20 a.m. at the restaurant in the 15-hundred block of Hwy 70 West.
Detectives said two men armed with a handgun climbed through a drive-through window while another man stood outside as lookout.
The manager and another employee were forced into the manager's office - where the manager was hit with the gun. The men then left with an undisclosed amount of cash.
Soon afterwards, a Wayne County deputy spotted a suspicious vehicle leaving the area and stopped it about a quarter mile away from the restaurant. A search of the car turned up the gun and some of the cash.
William Earl Warren Jr, 25, was charged with kidnapping, robbery, possession of stolen property, and possession of a weapon by a felon. His bond was set at $255,000.
Warrants have been issued for 25-year-old Joseph Simms. Police said he should be considered armed and dangerous.
Detectives are trying to identify the third person involved. Anyone with information is asked to contact the Goldsboro Police Department at (919) 705-6572 or Goldsboro Wayne County Crime Stoppers at (919) 735-2255.