Proton exchange membrane fuel cells have the potential for applications in energy conversion and energy storage, but their development has been impeded by problems with the membrane electrode assembly. Here, we demonstrate that a silicon-based inorganic-organic membrane offers a number of advantages over Nafion--the membrane widely used as a proton exchange membrane in hydrogen fuel cells--including higher proton conductivity, a lack of volumetric size change, and membrane electrode assembly construction capabilities. Key to achieving these advantages is fabricating a silicon membrane with pores with diameters of approximately 5-7 nm, adding a self-assembled molecular monolayer on the pore surface, and then capping the pores with a layer of porous silica. The silica layer reduces the diameter of the pores and ensures their hydration, resulting in a proton conductivity that is two to three orders of magnitude higher than that of Nafion at low humidity. A membrane electrode assembly constructed with this proton exchange membrane delivered an order of magnitude higher power density than that achieved previously with a dry hydrogen feed and an air-breathing cathode.