It happened at the APH Smoke Shop on Belmont and 9th just before 4 am Tuesday.
Officers say the employee was working when two people tried robbing the store by demanding money, which led to the shooting.
Police found the employee inside the store with a gunshot wound.
He was rushed to the hospital for treatment.
Police say the suspects left the scene. No description of them has been released.
Anyone with more information is asked to contact Fresno police.