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A series of phenolphthalein-based sulfonated poly(ether ether sulfone) (SPEES) membranes were synthesized by aromatic nucleophilic polymerization reaction. The degree of sulfonation was controlled by direct synthesis of sulfonated polymer, which leads to high thermal stability. The physicochemical properties of the SPEES membranes were studied in order to evaluate the suitability of these membranes in fuel cell applications. The ion-exchange capacity of the synthesized SPEES membranes was found in the range between 2.19 mequiv. g−1 and 2.35 mequiv. g−1. The morphology of the membranes was investigated with high-resolution scanning electron microscopy and confirmed the presence of hydrophilic domains that impart good proton conductivity. The membrane electrode assembly of SPEES-30 and SPEES-50 membranes has been successfully fabricated, where SPEES-50 produced a maximum peak power density of 643 mW cm−2 while applying in hydrogen–oxygen fuel cell.