A fuel cell system includes a fuel cell, a cathode inflow water amount determining portion that determines a cathode inflow water amount after activation of the fuel cell; an obtaining portion that obtains a pore total volume of the cathode side catalyst layer; an operating condition determining portion that determines, based on the determined cathode inflow water amount and the obtained pore total volume, an operating condition of the fuel cell that includes a current value of current that flows through the fuel cell and an upper limit value of a period of time for which the current flows, for bringing the cathode inflow water amount within a range that is equal to or less than the pore total volume; and an adjusting portion that adjusts the current value and the period of time for which current of the current value flows, such that the determined operating condition is realized.