We investigate the sputtering deposition as a tool for preparing Polymer Electrolyte Membrane Fuel Cell (PEMFC) electrodes with improved performance and catalyst utilization. Anodes of PEMFC with ultra-low loading of Pt (0.05mgcm−2) are developed by alternate sputtering of Pt and painting layers of carbon nanotube ink with Nafion directly on the gas diffusion layer. Sputter depositing alternate layers of Pt on carbon-Nafion layer (CNL) has increased the anode activity over single-layer Pt deposited anode due to improved porosity and the presence of Pt nanoparticles in the inner CNL. Also, we investigated the influence of Nafion content in the CNL. The optimal Nafion content giving less resistance and better performance in an anode is 29wt.%. This is significantly lower than for standard MEA anodes, indicating sufficient interfacial contact between each CNL. We studied the anodes prepared with 50wt.% Nafion, which revealed larger ohmic resistance and also, blocks the CNL pores reducing gas permeability. Excellent mass transfer and performance is obtained with three-layer Pt sputter deposited anode with CNL containing 29wt.% of Nafion.