Police said the clerk had gotten into an altercation with the suspect during the robbery at a gas station convenience store at State College Boulevard and Katella Avenue at about 3 a.m.
The suspect shot the clerk with a pellet gun and fled the scene. The clerk was taken to a local hospital in unknown condition.
Officers say the suspect is responsible for at least a dozen similar robberies over the last couple of months. Anyone with information is urged to call the Anaheim Police Department at (714) 765-1900.