Fuel cell system and method of controlling fuel cell

A fuel cell system 1 is provided with a fuel cell 10 provided with an air passage 10a, an air inflow path 21, an air outflow path 23, a compressor 22, a pressure regulating valve 24, a bypass passage 27, and a bypass valve 28. A first threshold value is calculated based on an FC inlet pressure-lower limit value. When it is judged that an FC inlet pressure-command value is lower than the first threshold value, feedback control of the opening degree of the pressure regulating valve is suspended without suspending feedback control of the opening degree of the bypass valve if it is judged that the FC pressure loss-lower limit value is larger than the bypass pressure loss-lower limit value, and feedback control of the opening degree of the bypass valve is suspended without suspending feedback control of the opening degree of the pressure regulating valve if it is judged that the bypass pressure loss-lower limit value is larger than the FC pressure loss-lower limit value.