It happened around 2:00 a.m. Thursday at the store at 7720 Ogontz Avenue.
Police say the first suspect, who was wearing a painter's mask, pulled up his black hooded sweatshirt and showed the clerk the grip of a handgun in his waistband.
The second suspect, who was covering his face with his arm, walked around the counter as the clerk took about $100 out of the register.
The first suspect grabbed the cash and both fled the store on foot.
The store clerk was not harmed.
The first suspect is described as black male, about 5'8" tall wearing a black hooded sweatshirt and burgundy sweatpants.
The second suspect is also described as a black male about 5'8" tall wearing a gray hooded sweatshirt and gray sweatpants.
Anyone with information is asked to call Philadelphia Police at 215-686-TIPS (8477) or submit a tip online.