The objective of this research is to characterize the performance degradation attributable to the shutdown operations of polymer electrolyte fuel cells and to explore possible methods of reducing such degradation. As a result, it was made clear that a sequence of shutting off the air supply prior to stopping the hydrogen supply was effective in mitigating such performance degradation. Diagnostic technology revealed that the performance degradation was mainly observed at the cathode catalyst and that it was caused by so-called reversal current, which was triggered by air that crossed leak from the cathode to the anode.