A fuel cell system allows suppression of the deterioration of a fuel cell even if a part of a membrane configuring the fuel cell is unavailable for power production. The fuel cell is configured with a membrane, and an anode and a cathode provided so as to sandwich the membrane, and produces electric power from reaction of reactive gases via the membrane when the reactive gases are supplied to the anode and the cathode. The fuel cell system is configured with the fuel cell, an MEA power production effective area calculating means for calculating an area of the membrane surface available for power production, an upper limit power producing current calculating means for controlling the total power production of the fuel cell based on the power production effective area calculated by the MEA power production effective area calculating means, and a current controller.