Permeability evolution in intact rock as a result of micro-crack propagation is fundamental in understanding fluid flow within the excavation damage zone (EDZ) around underground openings. A 2D grain-based discrete element method incorporating Voronoi joint model is used to simulate the permeability evolution with progressive damage in intact rock when it is subjected to incremental mechanical loading. The rock response during uniaxial and triaxial loadings is simulated with and without taking into account the hydro-mechanical interactions between fluid and solid part of the rock. The numerical experiment results show that when modeling the rock behavior under compression, ignoring the coupled damage-flow processes results in an inaccurate prediction of mechanical properties of rock such as the peak strength and the post-peak response. The stress-strain response of the sample indicates that an increase in the applied confining stresses increases both the strain hardening range and the peak strength. In addition, the Permeability of models during triaxial loading increases by up to 2.5 orders of magnitude prior to rupture of rock. Progressive development of fractures as a result of crack accumulation leads to over 3 orders of magnitude increase in post-failure permeability compared to the permeability at the peak stress. These changes have been reported from laboratory testing results as well as in-situ permeability measurements carried out in the damaged zones in tunnel boundary. It has been demonstrated that Voronoi joint model incorporated in a DEM-based code has capability to simulate stress-induced permeability change in the brittle rocks as a result of processes such as initiation, propagation, and accumulation of cracks.