Surface-patterned Nafion films were prepared by using different types of ZnO nanorods as templates for polymer electrolyte membrane fuel-cell (PEMFC) applications. Varying the concentrations of the Zn precursor produced ZnO nanorods with different diameters and pore sizes in the Nafion films. The surface-tuned structure of the films improved fuel-cell performance owing to effective Pt loading on the membranes through an enhancement in surface area. Also, the interconnected morphology resulted in a reduction in charge-transfer resistance at the interface between the electrode and membrane. The optimum surface-patterned Nafion film recorded a current density of 1.19 A cm−2 at 0.6 V and a maximum power density of 0.95 W cm−2. These values are much higher than those of non-patterned Nafion (0.85 A cm−2 and 0.59 W cm−2, respectively). We expect that the patterning process using ZnO nanorod templates will improve the performance of any electrochemical device by allowing for the tuning of the interfacial resistance.