Provided is a fuel cell system which can properly control a refresh operation. A controller controls the refresh operation so that an output voltage does not exceed an avoidance voltage even after the refresh operation. Specifically, the controller estimates the output voltage after the refresh operation from the output voltage before the refresh operation and controls execution of the refresh operation so that the estimated output voltage after the refresh operation does not exceed the avoidance voltage. For example, if before the refresh operation, when judging that the estimated output voltage after the refresh operation does not exceed the avoidance voltage, the controller executes the refresh operation.