A sound understanding of the water permeability evolution in fractured shale is essential to the optimal hydraulic fracturing (reservoir stimulation) strategies. We have measured the water permeability of six fractured shale samples from Qiongzhusi Formation in southwest China at various pressure and stress conditions. Results showed that the average uniaxial compressive strength (UCS) and average tensile strength of the Qiongzhusi shale samples were 106.3 and 10.131 MPa, respectively. The nanometre-sized (tiny) pore structure is the dominant characteristic of the Qiongzhusi shale. Following this, we proposed a pre-stressing strategy for creating fractures in shale for permeability measurement and its validity was evaluated by CT scanning. Shale water permeability increased with pressure differential. While shale water permeability declined with increasing effective stress, such effect dropped significantly as the effective stress continues to increase. Interestingly, shale permeability increased with pressure when the pressure is relatively low (less than 4 MPa), which is inconsistent with the classic Darcy's theory. This is caused by the Bingham flow that often occurs in tiny pores. Most importantly, the proposed permeability model would fully capture the experimental data with reasonable accuracy in a wide range of stresses.