There is disclosed a fuel cell system capable of drying a fuel cell in a short time after a system stop instruction is issued. The fuel cell system includes a controller to control the execution of a normal operation and a dry operation which decreases the water content of the fuel cell as compared with the normal operation. The controller executes the dry operation prior to the system stop instruction so that the water content of the fuel cell is decreased as compared with the normal operation at a time of the system stop instruction. The controller may execute the dry operation before the system stop instruction in a case where it is predicted that the temperature of the fuel cell at the system stop or the next system start is a predetermined low temperature.