The purpose of this work is to enhance the proton conductivity and fuel cell performance of sulfonated poly(phthalazinone ether ketone) (SPPEK) as a proton exchange membrane through the application of SrTiO3 perovskite nanoparticles. Nanocomposite membranes based on SPPEK and SrTiO3 perovskite nanoparticles were prepared via a casting method. The highest proton conductivity of nanocomposite membranes obtained was 120 mS cm−1 at 90 °C and 95% RH. These enhancements could be related to the hygroscopic structure of SrTiO3 perovskite nanoparticles and the formation of hydrogen bonds between nanoparticles and water molecules. The satisfactory power density, 0.41 W cm−2 at 0.5 V and 85 °C, of the nanocomposite membrane (5 wt% content of nanoparticles) confirms their potential for application in the PEM fuel cells.