The shooting occurred about 7:45 p.m. at the Super Save Food Store in the 2500 block of East Abram Street, near State Highway 360.
The clerk told police that two people went into the store with the intention of robbing him, but the clerk pulled out a gun and fatally shot one of the two men, police Lt. Christopher Cook said.
He was pronounced dead on the scene. The clerk told police the man was armed, but a firearm has not yet been located, he said.
Police have detained the second man, but will have to review surveillance footage to see whether he was involved in the robbery attempt, Cook said.
Another employee who was in the store at the time hid in the cooler during the incident