To improve an output of a fuel cell and power generation efficiency by enhancing drainage of the fuel cell upon actuation below freezing temperature. In a fuel cell system that generates power by supplying fuel gas and oxidant gas, the output of the fuel cell is measured when a temperature of the fuel cell after the actuation below freezing temperature exceeds 0 degree, and if a value of the output is equal to or less than a reference output value, pressure pulsation is applied to a cathode electrode to drain water built up in the fuel cell.