We initially prepared the sulfanilic acid functionalized poly(1,4-phenylene ether ether sulfone) (SPEES-SA) membrane, and it was further modified by incorporating the different mass% of sulfonic acid functionalized zeolites to develop the composite membranes. The functionalization of zeolites was confirmed by wide-angle X-ray diffraction and X-ray photoelectron spectroscopy. The resulting SPEES-SA and its composite membranes were subjected to various techniques to investigate their physico-chemical properties. The morphology of the membranes was studied using both atomic force microscopy and scanning electron microscopy. The performance of the membranes was studied in terms of swelling behavior, water uptake, ion exchange capacity and proton conductivity with respect to mass% of functionalized zeolites. The oxidative stability was performed in Fenton's solution at 80 °C and ascertained that more than 95% of the membrane residue remained with a minimum loss of ion exchange capacity (IEC). The proton conductivity data revealed that the membranes incorporated with 8 mass% of functionalized zeolites exhibited the highest IEC values. The proton conductivity of the composite membranes incorporated with functionalized Na-ZSM-5 zeolite, Na-Beta zeolite and Na-Mordenite zeolite was found to be 0.102, 0.112 and 0.124 S cm−1, respectively. The fuel cell performance study also revealed that composite membranes incorporated with 8 mass% of functionalized Na-ZSM-5 zeolite, Na-Beta zeolite and Na-Mordenite zeolite demonstrated excellent power density of 0.37 W cm−2 at 0.97 A cm−2, 0.42 W cm−2 at 1.05 A cm−2 and 0.45 W cm−2 at 1.1 A cm−2, respectively. These data are much superior to the commercially available Nafion® 117 membrane. Thus, the developed composite membranes are promising candidates for the applications of fuel cell technology.