This study encompasses a deep understanding of nanohybrid materials that are produced by combining an organic material with inorganic filler. This amalgamation of different organic and inorganic compounds is cheaper and has very good features that include membrane permeability, conductivity properties, stability, perfect water retention, and mechanical properties. There are many factors such as type and size of particles and their preparation techniques that greatly affect properties of nanohybrids. These nanohybrid materials are extensively being used in different applications for fuel cells that are thought to be efficient devices for converting chemical energy from a gaseous fuel other than conventional fossil fuel into electrical energy. It is anticipated that due to zero emissions, fuel cells will be replaced by rechargeable batteries and heat engines in near future. A complete note on the working principle and proton conduction mechanism in fuel cells is described in this study. Nafion membranes were conventionally used in fuel cells. Although these membranes provide attractively high conductivity, it also includes many problems such as fuel crossover, high cost, water handling, and CO poisoning that requires special attention. To address these problems, Nafion is combined with metal oxides, e.g., Fe2TiO5, ZrO2, CeO2, and TiO2 to get a modified Nafion-metal oxide nanohybrid. It is synthesized using water as solvent and has very good proton conductivity along with better mechanical strength and water retention ability. There are also many other nanohybrids, e.g., graphene-based nanohybrids, carbon nanotube-based nanohybrids, conducting polymer-based nanohybrids, novel green nanohybrids, etc., which can be replaced by simple Nafion-based nanohybrids in fuel cells to get more specified results. Major function of all these nanohybrid membranes is to minimize the flow of electrons and at the same time increasing the rate of flow of ions through it in any kind of fuel cell. Overall, in this study all types of nanohybrids are discussed for their applications in different types of fuel cells.