It happened at the Rodeway Inn on Blackstone and Ashlan Avenues shortly after 1:30 am.
Officers arrived to find a 49-year-old man in the parking lot shot in both of his legs. He was taken to Community Regional Medical Center and is expected to recover.
Police say the victim was able to tell officers what led up to the shooting.
"The initial information we got from the victim is that he was just standing in the parking lot, and for no apparent reason, a male adult walked to him and shot him in the legs and took off running," said Fresno Police Lt. Israel Reyes.
Police have not released a description of the suspect.