The armed suspect entered the business near Shaw and Marks around 7:30 p.m. on Monday.
Fresno police officers say he was wearing all black and had part of his face covered when he held the employee at gunpoint and demanded cash.
"We don't get a lot of robberies from restaurants so I think this is a big shock for them," said Lieutenant Jerardo Chamalbide.
The suspect was last seen running down Marks wearing a black hooded sweatshirt.
It's not clear how much cash they took off with from the business.
No one was injured during the armed robbery.