It happened at 3:39 a.m. Wednesday at the Sunoco APlus convenience store at 15 East Germantown Pike.
Police tell Action News the clerk was shot in the ankle by an armed robber.
Medics took the victim to Paoli Hospital, where he is listed in stable condition.
The employee told responding officers that three to five males wearing all black clothing rushed in the store, and forced him to open the register at gunpoint.
At some point in the incident the employee was shot.
The suspects then fled with an undetermined amount of cash and cigarettes.
A police investigation is underway.