The blaze was first reported around 7:30 a.m. at the hotel on Blackstone Avenue and Griffith Way.
Firefighters arrived to find flames in a single room and were able to keep the fire from spreading further into the building.
Dark smoke could be seen by people passing by the area. The smoke drifted across the motel, and water caused damage to the unit below the room where the fire started.
No one was injured.
Fresno Fire Battalion Chief Tim Fulmer said the people staying at the motel would be moved into another room.
The cause of the fire is under investigation.