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In the present work, different methanesulfonate-based protic ionic liquids (PILs) were synthesized and their structural characterization was performed using FTIR, ¹H, and ¹³C NMR spectroscopy. Their thermal behavior and stability were studied using DSC and TGA, respectively, and EIS was used to study the ionic conductivity of these PILs. The PIL, which was diethanolammonium-methanesulfonate-based due to its compatibility with polybenzimidazole (PBI) to form composite membranes, was used to prepare proton-conducting polymer electrolyte membranes (PEMs) for prospective high-temperature fuel cell application. The prepared PEMs were further characterized using FTIR, DSC, TGA, SEM, and EIS. The FTIR results indicated good interaction among the PEM components and the DSC results suggested good miscibility and a plasticizing effect of the incorporated PIL in the PBI polymer matrix. All the PEMs showed good thermal stability and good proton conductivity for prospective high-temperature fuel cell application.