A fuel cell system includes a fuel cell stack, a fuel gas supply channel, a fuel gas circulation channel, a circulating pump that is driven by a pump motor having no rotation detecting sensor, and an ECU. When a method for operating the fuel cell system determines that the circulating pump is frozen in a low-temperature environment, the method performs a first step of performing a brake mode to limit the rotation of the pump motor while passing current to the pump motor, to thereby heat the pump motor. The method further performs a second step of, after rotating the pump motor, determining that the circulating pump has unfrozen if the rotational speed of the pump motor exceeds a given value.