A fuel cell system configured to generate power by supplying anode gas and cathode gas to a fuel cell includes a cathode gas supply unit configured to supply the cathode gas to the fuel cell, a cathode pressure detection unit configured to detect a pressure of the cathode gas to be supplied to the fuel cell, a fuel cell temperature detection unit configured to detect a temperature of the fuel cell, an internal resistance detection unit configured to detect an internal resistance of the fuel cell, a target cathode flow rate calculation unit configured to calculate a target cathode flow rate necessary for supply to the fuel cell based on an operating state of the fuel cell system, a cathode flow rate estimation unit configured to estimate a flow rate of the cathode gas according to the pressure of the cathode gas, the temperature of the fuel cell and the internal resistance of the fuel cell, and a cathode flow rate control unit configured to control the cathode gas supply unit based on the target cathode flow rate and the estimated flow rate of the cathode gas.