It happened around 11 p.m. at the Lukoil gas station on the 4800 block of Tacony Street.
Police said the 20-year-old clerk went outside of the store to confront the three men when one pulled a gun and shot him.
He was taken to Temple University Hospital with a gunshot wound in his stomach. Officials said he is in stable condition.
Investigators said the three suspects ran away from the scene after the shooting. They are described as thin and were wearing dark clothing at the time of the incident.
Police are currently reviewing surveillance footage from inside the store.
Anyone with information is asked to contact the police.