A high-temperature polymer electrolyte membrane fuel cell (PEMFC) has enormous potential to produce clean energy with minimal environmental pollution along with high energy density and conversion efficiency. In the present work, anhydrous proton-conducting polymer electrolyte membranes for prospective high-temperature fuel cell application were successfully prepared using different protic ionic liquids (PILs) and sulfonated poly(ether ether ketone) (SPEEK). The protic ionic liquids (PILs), 2-hydroxyethylammonium formate, diethylmethyl ammonium triflate, 1-ethylimidazolium bis(trifluoromethylsulfonyl)imide, 1,2-dimethyl imidazolium bis(trifluoro methylsulfonyl)imide, and diethylmethylammonium methanesulfonate were selected based on their favorable physicochemical properties. The effect of the incorporation of the PIL on the structural, thermal, and electrical transport properties of the composite SPEEK polymer electrolyte membranes was studied. The prepared polymer electrolyte membranes (PEMs) were characterized using Fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray diffractometry (XRD), and electrochemical impedance spectroscopy (EIS) techniques. FTIR results indicated an interaction between the PIL and the SPEEK, which resulted in homogeneous and flexible membranes. The DSC results confirmed good miscibility and elucidated plasticizing effect of the incorporated PIL on the SPEEK polymer matrix. All the PEMs showed good thermal stability and high-temperature anhydrous proton conductivity, achieving best proton conductivity, ≈8 × 10–3 S cm−1 at 120 °C and low activation energy ≈0.26 eV, making it suitable for prospective high-temperature PEMFC applications.