It happened around 11:30 at the Circle 6 Store on Ventura and First Street in Southeast Fresno.
Authorities say an armed man walked into the store and demanded money. But after the clerk gave him an unknown amount of cash, he shot her.
The woman was taken to Community Regional Medical Center with non-life threatening injuries.
The gunman got away.
"Currently we do have officers in the area looking for the suspect. We are asking for the community's help with any information they have regarding the location of the suspect," Lt. Tom Rowe said.
Anyone with information about the shooting or the suspect is asked to call Fresno Police.