Hydrogen energy is converted to electricity through fuel cells, aided by nanostructured materials. Fuel cell technology is a promising method for utilizing energy sources, ensuring sustainability, and protecting the environment. However, it still faces drawbacks such as high cost, operability, and durability issues. Nanomaterials can address these drawbacks by enhancing catalysts, electrodes, and fuel cell membranes, which play a crucial role in separating hydrogen into protons and electrons. Proton exchange membrane fuel cells (PEMFCs) have gained significant attention in scientific research. The primary objectives are to reduce greenhouse gas emissions, particularly in the automotive industry, and develop cost-effective methods and materials to enhance PEMFC efficiency. We provide a typical yet inclusive review of various types of proton-conducting membranes. In this review article, special focus is given to the distinctive nature of nanomaterial-filled proton-conducting membranes and their essential characteristics, including their structural, dielectric, proton transport, and thermal properties. We provide an overview of the various reported nanomaterials, such as metal oxide, carbon, and polymeric nanomaterials. Additionally, the synthesis methods in situ polymerization, solution casting, electrospinning, and layer-by-layer assembly for proton-conducting membrane preparation were analyzed. In conclusion, the way to implement the desired energy conversion application, such as a fuel cell, using a nanostructured proton-conducting membrane has been demonstrated.