The robbery occurred at about 2:20 a.m. in the 6000-block of North Western Avenue.
Police said two suspects entered the store, showed a handgun and demanded that the clerk open the register.
The clerk complied, but was then struck in the head with the gun and dragged into the back area of the store, police said.
The suspects then grabbed cash and fled the store. No one is in custody.
The clerk refused medical treatment.