Authorities said one of the men brandished a handgun and hit the clerk on top of his head while the other two suspects emptied the register of an unknown amount of cash.
The trio fled the store on foot.
The clerk was left with a minor abrasion on his head and was treated at the scene by paramedics.
Anyone with information on the robbery or suspects is asked to call Simi Valley police at (805) 583-6950.