It happened around 2:00 a.m. Monday at the Pretzel Factory in the 1600 block of Grant Avenue.
The two men, wearing hoodies and black jeans, made off with a cash register and an unknown amount of cash.
Officers remained on the scene investigating.
They are now going over surveillance video as the search for the suspects continues.
Anyone with information is urged to contact Philadelphia Police at 215-686-TIPS (8477), text a tip to PPD TIP (773847) or through PhillyPolice.com.