Cobalt oxide silica membranes were prepared and tested to separate small molecular gases, such as He (dk = 2.6 Å) and H2 (dk = 2.89 Å), from other gases with larger kinetic diameters, such as CO2 (dk = 3.47 Å) and Ar (dk = 3.41 Å). In view of the amorphous nature of silica membranes, pore sizes are generally distributed in the ultra-microporous range. However, it is difficult to determine the pore size of silica derived membranes by conventional characterization methods, such as N2 physisorption-desorption or high-resolution electron microscopy. Therefore, this work endeavors to determine the pore size of the membranes based on transport phenomena and computer modelling. This was carried out by using the oscillator model and correlating with experimental results, such as gas permeance (i.e., normalized pressure flux), apparent activation energy for gas permeation. Based on the oscillator model, He and H2 can diffuse through constrictions narrower than their gas kinetic diameters at high temperatures, and this was possibly due to the high kinetic energy promoted by the increase in external temperature. It was interesting to observe changes in transport phenomena for the cobalt oxide doped membranes exposed to H2 at high temperatures up to 500 °C. This was attributed to the reduction of cobalt oxide, and this redox effect gave different apparent activation energy. The reduced membrane showed lower apparent activation energy and higher gas permeance than the oxidized membrane, due to the enlargement of pores. These results together with effective medium theory (EMT) suggest that the pore size distribution is changed and the peak of the distribution is slightly shifted to a larger value. Hence, this work showed for the first time that the oscillator model with EMT is a potential tool to determine the pore size of silica derived membranes from experimental gas permeation data.