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′). A controlled-oxidant flow device (209) near an oxygen source (58′) permits a minimal amount of atmospheric oxygen to enter the power plant (200) during shut down to equalize pressure between ambient atmosphere and the flow paths (24′, 28′) and to keep limited atmospheric oxygen entering the power plant (200) through the device (209) as far as possible from fuel cell flow fields (28′, 42′). A non-leaking hydrogen inlet valve (202), a non-leaking cathode exhaust valve (208), and a combined oxidant and fuel exhaust line (206) also minimize penetration of oxygen into the shut down power plant (200).