The polymer electrolyte membrane (PEM) is a key component in the PEM fuel cell (PEMFC) system. This study highlights the latest development of PEM technology by combining Nafion® and ionic liquids, namely 2–Hydroxyethylammonium Formate (2–HEAF) and Propylammonium Nitrate (PAN). Test membranes were prepared using the casting technique. The impact of functional groups in grafting, morphology, thermal stability, ion exchange capacity, water absorption, swelling and proton conductivity for the prepared membranes is discussed. Both hybrid membranes showed higher values in ion exchange capacity, water uptake and swelling rate as compared to the recast pure Nafion® membrane. The results also show that the proton conductivity of Nafion®/2–HEAF and Nafion®/PAN membranes increased with increasing ionic liquid concentrations. The maximum values of proton conductivity for Nafion®/2–HEAF and Nafion®/PAN membranes were 2.87 and 4.55 mScm−1, respectively, equivalent to 2.2 and 3.5 times that of the pure recast Nafion® membrane.