A fuel cell system comprising: a fuel cell; an air supply flow path configured to supply air to the fuel cell; an air discharge flow path configured to discharge the air from the fuel cell; a compressor configured to supply the air to the air supply flow path; a motor configured to drive the compressor; a turbine disposed in the air discharge flow path to assist driving of the compressor by the motor; a bypass flow path configured to bring a downstream side of the compressor in the air supply flow path into communication with an upstream side of the turbine in the air discharge flow path; a bypass valve configured to open and close the bypass flow path; and a controller configured to control driving of the motor and opening and closing of the bypass valve according to a required air flow rate that is an air flow rate required for power generation of the fuel cell, wherein when the required air flow rate is equal to or higher than a predetermined threshold value, the controller performs a first control in which (i) the bypass valve is closed and (ii) the driving of the motor is controlled to cause the air to flow through the fuel cell at a flow rate corresponding to the required air flow rate, and when the required air flow rate is lower than the predetermined threshold value, the controller performs a second control in which (i) the bypass valve is opened to cause the air to also flow through the bypass flow path and (ii) the driving of the motor is controlled to cause the air to flow through the fuel cell at the flow rate corresponding to the required air flow rate, characterized in that: the predetermined threshold value is a value determined based on a flow rate at which power consumption of the motor with respect to a flow rate of air discharged from the compressor in the fuel cell system becomes minimal. a fuel cell; an air supply flow path configured to supply air to the fuel cell; an air discharge flow path configured to discharge the air from the fuel cell; a compressor configured to supply the air to the air supply flow path; a motor configured to drive the compressor; a turbine disposed in the air discharge flow path to assist driving of the compressor by the motor; a bypass flow path configured to bring a downstream side of the compressor in the air supply flow path into communication with an upstream side of the turbine in the air discharge flow path; a bypass valve configured to open and close the bypass flow path; and a controller configured to control driving of the motor and opening and closing of the bypass valve according to a required air flow rate that is an air flow rate required for power generation of the fuel cell, wherein when the required air flow rate is equal to or higher than a predetermined threshold value, the controller performs a first control in which (i) the bypass valve is closed and (ii) the driving of the motor is controlled to cause the air to flow through the fuel cell at a flow rate corresponding to the required air flow rate, and when the required air flow rate is lower than the predetermined threshold value, the controller performs a second control in which (i) the bypass valve is opened to cause the air to also flow through the bypass flow path and (ii) the driving of the motor is controlled to cause the air to flow through the fuel cell at the flow rate corresponding to the required air flow rate, characterized in that: the predetermined threshold value is a value determined based on a flow rate at which power consumption of the motor with respect to a flow rate of air discharged from the compressor in the fuel cell system becomes minimal.