Combination of inorganic fillers into organic polymer membranes (organic–inorganic hybrid membranes) has drawn a significant deal of attention over the last few decades. This is because of the incorporated influence of the organic and inorganic phases towards proton conductivity and membrane stability, in addition to cost decline, improved water retention property, and also suppressing fuel crossover by increasing the transport pathway tortuousness. The preparation methods of the composite membranes and the intrinsic characteristics of the used particles as filler, such as size, type, surface acidity, shape, and their interactions with the polymer matrix can significantly affect the properties of the resultant matrix. The membranes currently used in proton exchange membrane fuel cells (PEMFCs) are perfluorinated polymers containing sulfonic acid, such as Nafion®. Although these membranes possess superior properties, such as high proton conductivity and acceptable chemical, mechanical, and thermal stability, they suffer from several disadvantages such as water management, CO poisoning, and fuel crossover. Organic-inorganic nanocomposite PEMs offer excellent potentials for overcoming these shortcomings in order to achieve improved FC performance. Various inorganic fillers for the fabrication of composite membranes have been comprehensively reviewed in the present article. Moreover, the properties of polymer composites containing different nanoparticles have been thoroughly discussed.