This work reports the preparation of Nafion/zeolite composite membranes with different zeolite loading. The structure of the Nafion/zeolite composite membranes are investigated by Scanning Electron Microscopy (SEM), X-Ray Diffraction (XRD) and by thermogravimetric analysis (TGA). The introduction of zeolite particles into the Nafion matrix helps to improve the water uptake, proton conductivity and thermal stability of the nanocomposite membranes compared to the virgin Nafion membrane. The SEM analyses have proved the uniform and homogeneous distribution of zeolite in composite membranes. The composite membranes are tested in a single PEMFC with a 5 cm² active area operating at the temperature range of 75–120 °C and in humidified under 50% relative humidity (RH) and fully humidified conditions. Single PEMFC tests show that Nafion/zeolite composite membrane is more stable and also performed better than virgin Nafion membrane at low humidity condition. The results indicate the Nafion/zeolite composite membranes could be utilized as the proton exchange membranes for PEMFC.