Disclosed is a fuel cell system provided with a fuel cell (1), a water tank (2) which stores water to be supplied to the fuel cell, and a heating device (10) which defrosts the water inside the tank during activation of the fuel cell. The fuel cell system has a switch (19) which signals activation of the fuel cell; at least one temperature sensor (13, 14) which detects a temperature inside the water tank; a pump (3) which conveys water from the water tank to the fuel cell; a heater (12) which warms the pump; and a controller (15). The controller (15) is programmed to read a start temperature from said at least one temperature sensor (13, 14) upon reception of a signal from the switch (19); calculate on the basis of the read start temperature a first warm-up period (tw) required for the water inside the water tank (2) to reach a predetermined temperature (Tw) greater than zero degrees centigrade; calculate on the basis of the read start temperature a second warm-up period (tH) required to defrost ice inside the pump (3) using the heater; set a start time (t2) for warm-up of the pump (3) using the heater on the basis of a difference (Dt) between the first warm-up period (tw) and the second warm-up period (tH); and control the heater to begin generating heat at the start time (t2) for warm-up of the pump (3).