A new approach to fabricating planar micro-fuel cells with flow channels and catalyst layers fully integrated into the Nafion membrane is presented. The microfabrication approach leverages the use of electron beam lithography for pattern creation, dry etching for pattern transfer and aspect ratio manipulation, and masking for selective electro-catalyst layer deposition. Sputtered Pt and conventional Pt/C served as catalyst layers for the fabricated cells which were tested under humid and dry conditions. The sputtered cell had the best overall performance. The maximum power densities were respectively 11.2 and 20.8 mW cm−2 for the dry and humidified conventional catalyst based cells, and 3.0 and 22.1 mW cm−2 for the sputtered Pt cells. Based on these results, the authors conclude that the observed performance is limited by ohmic polarization.