Fuel cell system and control method for same

A fuel cell system, including: a fuel cell having at least one combination of an electrolyte membrane and a cathode-side catalyst layer and an anode-side catalyst layer that have a plurality of pores; a control unit that operates the fuel cell such that an output current determined in accordance with an external load is output from the fuel cell; and an output current acquisition unit that acquires an output current of the fuel cell; wherein, when the control unit determines that an anode in-flowing water amount, which flows to the anode-side catalyst layer when the fuel cell continues power generation at a first output current acquired at a prescribed timing, exceeds a prescribed anode-side allowable water amount, the control unit performs current limitation control to operate the fuel cell at a second output current that is higher than the first output current, regardless of a requirement of the external load.