The effect on the gas permeance properties and structural morphology of the presence of methyl functional groups in a silica membrane was studied. Membranes were synthesized via chemical vapor deposition (CVD) at 650 °C and atmospheric pressure using three silicon compounds with differing numbers of methyl- and methoxy-functional groups: tetramethyl orthosilicate (TMOS), methyltrimethoxysilane (MTMOS), and dimethyldimethoxysilane (DMDMOS). The residence time of the silica precursors in the CVD process was adjusted for each precursor and optimized in terms of gas permeance and ideal gas selectivity criteria. Final H₂ permeances at 600 °C for the TMOS-, MTMOS-, and DMDMOS-derived membranes were respectively 1.7 × 10⁻⁷, 2.4 × 10⁻⁷, and 4.4 × 10⁻⁸ mol∙m⁻²∙s⁻¹∙Pa⁻¹ and H₂/N₂ selectivities were 990, 740, and 410. The presence of methyl groups in the membranes fabricated with the MTMOS and DMDMOS precursors was confirmed via Fourier-transform infrared (FTIR) spectroscopy. From FTIR analysis, an increasing methyl signal in the silica structure was correlated with both an improvement in the hydrothermal stability and an increase in the apparent activation energy for hydrogen permeation. In addition, the permeation mechanism for several gas species (He, H₂, Ne, CO₂, N₂, and CH₄) was determined by fitting the gas permeance temperature dependence to one of three models: solid state, gas-translational, or surface diffusion.