A fuel cell system and method in which the fuel cell system receives and an input oxidant gas and an input fuel gas, and in which a fuel processing assembly is provided and is adapted to at least humidify the input fuel gas which is to be supplied to the anode of the fuel cell of the system whose cathode receives the oxidant input gas via an anode oxidizing assembly which is adapted to couple the output of the anode of the fuel cell to the inlet of the cathode of the fuel cell during normal operation, shutdown and restart of the fuel cell system, and in which a control assembly is further provided and is adapted to respond to shutdown of the fuel cell system during which input fuel gas and input oxidant gas cease to be received by the fuel cell system, the control assembly being further adapted to, when the fuel cell system is shut down: control the fuel cell system so as to enable a purging gas to be able to flow through the fuel processing assembly to remove humidified fuel gas from the processing assembly and to enable a purging gas to be able to flow through the anode of the fuel cell.