A fuel cell system comprises: a fuel cell stack; a turbo compressor configured to supply a cathode gas to the fuel cell stack through a cathode gas supply line; a pressure regulation valve configured to regulate a pressure of the cathode gas; and a controller, wherein the controller is configured to calculate a target rotation speed of the turbo compressor and a target opening position of the pressure regulation valve, based on a target flow rate of the cathode gas and a target pressure of the cathode gas that are determined according to a required power output of the fuel cell stack and to control the turbo compressor and the pressure regulation valve using the calculated target rotation speed and the calculated target opening position, and the controller is configured, upon increase of the required power output, to: (a) determine an acceptable overshoot level of a flow rate of the cathode gas that is to be supplied to the fuel cell stack, the acceptable overshoot level being selected from a plurality of levels based on at least an increased amount of the required power output; and (b) set a time change in opening position of the pressure regulation valve such that an overshoot amount in a change of the flow rate of the cathode gas becomes smaller as the acceptable overshoot level gets lower, and perform control of the pressure regulation valve. This configuration suppresses an excessive overshoot in the flow rate of the cathode gas.