A fuel cell system is provided that can suppress the degradation of the MEA and simultaneously assure the merchantability. The fuel cell system 1 includes: a fuel cell 10 that generates electric power by reacting hydrogen gas and oxidant gas; a temperature sensor 103 that detects the temperature of the fuel cell 10; a voltage lower limit calculation portion 31 that sets the voltage threshold to limit the output of the fuel cell 10 based on the temperature detected of the fuel cell 10; a current upper limit calculation portion 32 and the current limiting portion 33 that limits the output of the fuel cell in a case where the voltage generated by the fuel cell 10 is lower than the voltage threshold.