A fuel cell system includes an auxiliary machine electrically connected to a fuel cell, the auxiliary machine being driven by power of the fuel cell, a heater electrically connected to the fuel cell, the heater being configured to heat cooling water supplied to the fuel cell, and a warm-up control unit configured to warm up the fuel cell itself by the supply of power to the auxiliary machine and the heater during start-up of the fuel cell below freezing point. The warm-up control unit includes a water amount computation unit configured to compute a produced water amount on the basis of a degree of wetness and a temperature of the fuel cell and a generated power of the fuel cell during warm-up, the produced water amount being a water amount produced in an electrolyte membrane until the temperature of the fuel cell increases to a freezing point temperature, and an anti-freezing control unit configured to increase a power ratio of power to the heater in regards to the auxiliary machine during the warm-up when the computed produced water amount is determined to be larger than a threshold value.