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A portion of natural fractures may become re-activated during hydraulic fracturing treatment in deep sedimentary enhanced geothermal systems (EGS), dependent on their geometry and orientation, among other factors. While the stress-dependency of natural fractures in low-permeability sedimentary rocks has been the subject of many studies, very few experimental works have met the considerable technical challenge of measuring permeability during fracturing process. This experimental study investigates the evolution of natural fractures permeability in low-permeability sedimentary rocks during fracturing process with examples from low-permeability siltstones (Canadian Montney Formation). The primary objective was to evaluate the mechanisms that control natural fracture permeability due to fracture tip extension and/or fracture aperture dilation during fracturing. Experimental observations indicated that the permeability of fractured core (∼1 md) was significantly, about two orders of magnitude, larger than that of intact core (∼0.01 md) but only about 2–4 times larger than that of partially-fractured core (0.2–0.4 md). Notably, the geometries of the induced fractures differed significantly between the intact (rough and zigzagged) and partially-fractured (smooth with straight aperture) cores. The outcomes of this study could be important for assessing the evolution of natural fracture permeability during hydraulic fracturing in deep sedimentary EGS.