The incident happened about 3pm on Monday when a man entered the shop on South Terrace, threatened staff and left with a number of tablets.
A description of the suspect was circulated to gardaí on duty in the area.
Gardaí then met a man in his 20s who fitted the description of the suspect following a patrol.
He was arrested and questioned at Bridewell Garda station.
The man is due to appear before Cork City District Court on Tuesday morning.