The purification of hydrogen rich gases is of great technological importance in the “hydrogen economy” and is achieved by selective membranes made of organic or inorganic materials. In this field, a strong challenge is the synthesis of defect-free ultrathin Pd-based selective membranes. We present a study on the synthesis and performances of a bilayer structure consisting of 100 nm nanoporous silica coated with a 150 nm Pd–Ag layer. An alumina disk having periodic microsieves structure was used as support for the bilayer. The hydrogen transport through this nanocomposite membrane is controlled by the dissociation of molecular hydrogen at the surface of the Pd–Ag functional layer. When operating at 573 K, the membrane exhibits high H2/N2 selectivity (a factor as high as 600–900), high H2 permeance (∼10−6 mol m−2 s−1 Pa−1), and operative stability on long-term operations.