A fuel cell system includes a fuel feeder that supplies fuel, a fuel cell stack that generates power through an electrochemical reaction using air and a hydrogen-containing gas generated from the fuel, a first temperature sensor that senses the temperature of the fuel cell stack, and a controller. The fuel cell stack has a membrane electrode assembly including an electrolyte membrane through which protons can pass, a cathode on one side of the electrolyte membrane, and an anode on the other side of the electrolyte membrane. The controller defines an upper limit of current output from the fuel cell stack on the basis of the temperature of the fuel cell stack, the supply of the fuel, and the hydrogen consumption of the fuel cell stack associated with internal leakage current and keeps the current output from the fuel cell stack at or below the upper limit.