A low temperature PEM fuel cell system is prevented against freezing after a shutdown in sub-freezing conditions. The fuel cell can be heated by filling an anode chamber with a fuel (the hydrogen or a hydrogen-rich reactant gas) and generating the hydrogen on a cathode. A defined amount of air is supplied to the cathode chamber. The fuel cell is locally heated to a defined temperature by the exothermic chemical reaction between the hydrogen and the oxygen on a cathode catalyst. Once the fuel cell is warmed to the defined temperature, the hydrogen generation on the cathode and the air supply can be discontinued. Water formed at the cathode can be evaporated by means of pre-heating of an air flow. This procedure provides plain saturation of the cathode with the hydrogen and, as result, mild, safe heating the fuel cell without use of an additional external power supply.