When starting operation of a fuel cell below the freezing point, a fuel cell system adjusts the open degree of a hydrogen pressure adjusting valve, introduces hydrogen to a hydrogen entrance of the fuel cell so as to make the total pressure of the hydrogen entrance a first pressure, and starts a hydrogen circulation pump. If at least one of the cell voltages acquired by a cell voltmeter is below a predetermined voltage, the system determines that clogging is caused in a hydrogen flow channel in the fuel cell. When it is determined that clogging is present, the open degree of the pressure adjusting valve is adjusted and hydrogen is introduced to the hydrogen entrance so that the total pressure of the hydrogen entrance is a second pressure which is higher than the first pressure. Then, the hydrogen circulation pump is stopped and the fuel cell is warmed up to dissolve the clogging of the hydrogen flow channel. Thus, it is possible to suppress degradation of the fuel cell upon an operation start below the freezing point.