Polymer electrolyte fuel cells (PEFCs) are drawing attention as energy conversion devices for next generations because of their highly efficient, environmentally benign, and portable features. In the last five decades, three distinguishable innovations were achieved in terms of proton conductive membranes and electrodes: introduction of perfluorinated membranes into PEFCs, adoption of ionomers for electrodes, and increased toughness of membranes by reinforced membranes. The efficiency, cost, and durability achieved from the past three innovations are still not enough to replace competing technologies such as combustion engines. In this review, the authors would elucidate the three different methods based on nanotechnology to overcome the limits: nanoporous carbon-supported catalysts, nanocomposite membranes, and nanostructured membrane electrode assemblies, which will bring the fourth innovation to PEFCs. With the innovation, PEFCs will fulfill the goals of being clean-energy conversion devices in the major applications of stationary, portable, and vehicle markets.