Proton-exchange membrane fuel cells (PEMFCs) are regarded as promising alternatives to internal combustion engines (ICEs) to reduce pollution. Recent research on PEMFCs focuses on achieving higher power densities, reducing the refueling time, mitigating the final price, and decreasing the degradations, to facilitate the commercialization of hydrogen mobility. The design of bipolar plates and compression kits, in addition to their coating, can effectively improve performance, increase durability, and support water/thermal management. Past reviews usually focused on the specific aspect, which can hardly provide readers with a complete picture of the key challenges facing and advances in the long-term performance of PEMFCs. This paper aims to deliver a comprehensive source to review, from both experimental, analytical and numerical viewpoints, design challenges, degradation modeling, protective coatings for bipolar plates, and key operational challenges facing and solutions to the stack to prevent contamination. The significant research gaps in the long-term performance of PEMFCs are identified as (1) improved bipolar-plate design and coating, (2) the optimization of the design of sealing and compression kits to reduce mechanical stresses, and (3) stack degradation regarding fuel contamination and dynamic operation.