The incident occurred at 1:55 a.m. at Greg's Gas Plus on Richland Avenue, said Aiken Department of Public Safety Lt. David Turno.
Lt. Turno said the clerk described the suspects as two black males wearing dark clothing, possibly driving a late model, blue four-door Chevrolet Impala or Malibu with a Georgia tag.
Authorities say they don't think this case is connected to another armed robbery that took place yesterday afternoon at a gas station on Whiskey Road.
Anyone with information is asked to call the Aiken Department of Public Safety at (803) 642-7620 or Crimestoppers of the Midlands at (888) CRIME SC. Callers can remain anonymous and will be eligible for a cash reward of between $50 and $1,000.