The apparent gas permeability of shale is determined by both the intrinsic permeability and the gas flow regimes. Although a considerable amount of studies has been conducted to understand how flow regimes affect the apparent permeability, the impact of the intrinsic permeability has not been understood well. In this study, we introduced an intrinsic permeability model under variable stress conditions and the impact of the adsorbed layer thickness into a typical apparent permeability model. Our model was verified through comparisons of our model results with the experimental data in the literature. The new apparent permeability model was applied to evaluate the evolution of shale permeability under a spectrum of boundary conditions from stress-controlled to displacement-controlled conditions. Our model results demonstrate that the evolution of gas permeability is controlled by the change in intrinsic permeability under high pressures and by the flow regimes under low pressures. Because the change in intrinsic permeability is dependent on the boundary conditions, the evolution of apparent gas permeability is also boundary-dependent. When the shale is stress-controlled, the gas permeability increases with pressure under the constant confining stress condition. When the shale is under displacement-controlled, the gas permeability decreases with pressure under the constant volume condition.