We have successfully developed miniature hydrogen-air proton exchange membrane (PEM) fuel cells (FC) on silicon and poly-dimethylsiloxane (PDMS) base substrates using conventional and non-conventional microfabrication technologies. Prototype base substrates were fabricated by using well-known micromachining technologies, such as photolithography, deep reactive ion etching, and soft lithography. Sputtering, a physical vapor deposition method, was used to deposit catalysts and electrodes directly on the surface of the Nafion PEM. This paper describes the novel microfabrication approaches employed to selectively deposit electrodes and catalyst materials on the membrane with improved morphology and structure of electrodes. The aim was to reduce precious metal catalyst loadings, ohmic (iR) losses, and to improve structural support for the thin-film FC with concurrent reduction in fabrication complexity.