SPEEK polymer based thermally crosslinked polymer membranes are prepared by sol‐gel synthesis using kaolinite and sepiolite clays as additives. Characterization tests, ie, mechanical stability, thermal gravimetric analysis, ion exchange capability, swelling properties, water uptake capacities, electrochemical impedance spectroscopy analysis, and Fourier transform infrared spectroscopy (FTIR) analysis of the membranes were conducted. The sepiolite and kaolinite addition enhanced the thermal stability and the thermal crosslinking reduced the swelling capacity of the synthesized membranes. Proton conductivity results were increased from 0.172 to 0.268 S cm−1 by adding 9% of kaolinite, and to 0.329 S cm−1 at 80°C by adding 9% of sepiolite to the SPEEK membrane's polymer structure. The fuel cell current density and potential measurements of 141 mA cm−2 and 84.6 mW cm−2 were found respectively at 0.6 V for the SPEEK/S9 membrane, whereas values of 600 mA cm−2 and 348 mW cm−2 were found for the Nafion commercial membrane.