It happened just after 4:30 a.m. in the 2900 block of Welsh Road.
The 7-11 was closed for business early Friday morning as investigators searched for evidence from an armed robbery.
The 60-year-old clerk told police he was inside the store alone when two men wearing black ski masks came into the store on the 2900 block of Welsh Road and announced a robbery.
"The suspects approached clerk, put gun to his head, then struck the clerk in the back of his head, knocking him to ground," said Chief Inspector Scott.
The suspects tied his wrists behind his back with plastic zip ties. Police say the men were in the store for around 10 minutes, stealing a large amount of cigarettes and all of the cash from the register.
The clerk was able to free one of his hands to call 911 around 4:45 a.m.
Regular customers who have come to know and like the clerk are stunned.
"He's a great guy. I've come in here many nights. He's a hard worker. He's working five, six, seven days a week," said Colin Kenny.
"When I would go to work early in the morning, I would go in and talk to him all the time. I was a victim of a crime, and he was always telling me to be careful because I leave for work at 10:30 at night. And when I heard this, I was really shocked," said June Pommer.
The store is equipped with surveillance cameras on the inside and outside. Police are reviewing images captured by those cameras for more clues, but so far no video has been released.
The clerk was treated at the scene for cuts and bruises to his face and the back of his head. He declined to be taken to the hospital, but is expected to make a full recovery.
Police believe the thieves made off with between $80 and $100.
Anyone with information is asked to contact Philadelphia Police.