A control unit comprised in a fuel cell system is configured to perform prediction of whether a required output for a motor generator has a positive value and determination of whether a voltage of a fuel cell is less than a target voltage during execution of an auxiliary machine power consumption, and is configured to set a bypass valve to a first degree of opening during execution of the auxiliary machine power consumption when a result of at least one of the prediction and the determination is negative, and is configured to set the bypass valve to a second degree of opening less than the first degree of opening during execution of the auxiliary machine power consumption when results of both the prediction and the determination are positive.