The present invention is to prevent the temperature of an electric heater from being higher than or equal to a temperature at which control to reduce power consumption is started to prevent an abrupt decrease in the power consumption of the electric heater in order to secure a power consuming destination of a fuel cell. A fuel cell system 10 includes: a fuel cell 20 that receives the supply of reactant gas to generate power; a fuel cell cooling system 30 for circulating a coolant through the fuel cell 20 to cool the fuel cell 20; an electric heater 40 operated to consume power of the fuel cell 20 and driven to decrease power consumption abruptly at a temperature lower than a decomposition temperature of the coolant; and a heater cooling system 50 for circulating the coolant around the electric heater 40 to cool the electric heater 40. In a control method therefor, when the temperature of the coolant in the heater cooling system 50 falls within a temperature range where the power consumption of the electric heater 40 changes abruptly, the coolant is circulated from the fuel cell cooling system 30 into the heater cooling system 50 to cool the electric heater 40.