The objective of this study is to determine the durability of polymer electrolyte membrane fuel cells (PEMFCs) in constant current operation incorporated with regular recovery protocol for eliminating reversible performance loss of membrane electrode assemblies. Effects of operation ‘shunt current protocol’ on PEMFC durability are studied through analyses of the main degradation mechanism based on results of electrochemical characterizations and post-mortem investigations. The voltage of the protected cell using the shunt current protocol is stably preserved under the applied current density for 700 h with less degradation (4.2% of decay ratio), while the performance of the unprotected cell steadily decreased with time (15.1% over 700 h). The substantial performance deterioration of the unprotected cell is mainly attributed to morphology deterioration of the cathode catalyst layer with oxidation of Pt catalysts and chemical degradation of ionomers caused by generation of excessive water from electrochemical oxygen reduction reactions under high-humidity operating conditions. In contrast, the shunt current protocol plays an important role in sustaining high oxygen activity at the cathode catalyst surface, detaching partially covered OH− species on Pt active sites from water oxidation during cell operation caused by periodically applied shunt current for a very short period of 1 s every 5 h. We hope to provide insight into the operation protocol to extend the lifetime of PEMFCs, minimizing conversion from recoverable performance loss to irreversible (permanent) degradation during operation.