The permeation, hydrothermal stability (steam resilience) and regeneration behaviour of carbonised template molecular sieve silica (CTMSS) membranes were tested in this work for hydrogen purification in fuel cell fuel processing systems. A hydrostable CTMSS membrane was made using a novel surfactant templating procedure and compared with a standard non-templated molecular sieve silica (MSS) membrane. The MSS membrane H2 permeance and H2/CO permselectivity at 200 °C were in the order of 4.8 × 10−8 mol m−2 s−1 Pa−1 and 16, respectively. The hydrostable CTMSS membrane compared quite closely at the same conditions, having a H2 flux and H2/CO permselectivity of 2.1 × 10−8 mol m−2 s−1 Pa−1 and 13, respectively. When exposed to synthetic reformate gas, both membranes showed similar results to those obtained in pure gas streams. After steam was introduced at 34 mol%, the MSS membrane H2/CO selectivity dropped to half its original value, while the hydrostable CTMSS membrane showed no major selectivity variation. Permeation decreased with time regardless of the membrane tested, indicating the effect of water on silica films. Upon regeneration, the CTMSS membrane H2 permeance returned to its originally tested value, while the standard MSS membrane showed no improvement. As steam is present in gas reforming for fuel cells application, the hydrophobic template modifications are essential for stable membrane operation.