The fabrication and performance evaluation of miniature fuel cells on silicon wafers are presented in this paper. The miniature fuel cells consisted of a membrane–electrode-assembly (MEA) between two silicon substrates. The feed holes and channels in the silicon wafers, acting as a fuel distributor, were prepared by anisotropic silicon etching from the back and front of the wafer using silicon dioxide as an etching mask. In an attempt to reduce the cell resistance and consequently improving cell performance of the miniature silicon wafer fuel cell, a Cu/Au composite layer was sputtered on the top of silicon wafers as a current collector. Testing results show that (i) the cell performance was improved by increasing the thickness of the composite layer on the silicon wafer, and (ii) the miniature silicon wafer fuel cell with smaller size channels gave a better performance at the diffusion-limiting current region.