It happened inside the store located on the 6900 block of Caster Avenue early Tuesday morning.
Surveillance video shows the suspect walk in and lift his shirt to show that he had a gun.
He allegedly told the clerk, "We can do this the easy way or the hard way."
The 27-year-old clerk opened three cash registers and handed over an unknown amount of cash to the thief.
If you have any information about this crime or this suspect, please contact Northeast Detective Division at (215) 686-3153.