Silicon-based fuel cells are under active development for chip-scale electrical power supply. One of the greatest challenges in micro-fuel-cell research is the development of a suitable proton conducting membrane material that is compatible with standard silicon microfabrication technology. In this paper, the use of nanoporous silicon as a novel proton conducting membrane material in a microscale fuel cell membrane electrode assembly (MEA) is demonstrated. The devices were fabricated by first creating 100-μm-thick silicon windows in a standard silicon wafer, anodizing to create pores in the windows, and then painting catalyst layers and insulators onto the porous structures. Using 5 M formic acid and 0.5 M sulfuric acid as the fuel, the fuel cell peak power density reached about 30 mW/cm2 at current density level of about 120 mA/cm2. These results represent the successful integration of a new class of protonic conductor into a microfabricated silicon fuel cell.