The invention is a hydrogen passivation shut down system for a fuel cell power plant (10, 200). During shut down of the plant (10, 200), hydrogen fuel is permitted to transfer between an anode flow path (24, 24′) and a cathode flow path (38, 38′) while a low-pressure hydrogen generator (202) selectively generates an adequate amount of hydrogen and directs flow of the low-pressure hydrogen into the fuel cell (12′) downstream from a hydrogen inlet valve (52′) to maintain the fuel cell (12′) in a passive state.