Fluid flow in rock fractures is significantly influenced by cyclic shear. This phenomenon arises due to seismic activity or repeated stress changes resulting from excavation, blasting, and operational loads. In this study, experiments are carried out to investigate non-Darcian flow in single rough fractures after cyclic shearing. The evolution of inertial and viscous permeability is analyzed, and a predictive model for non-Darcian flow is established. Cyclic shearing experiments are first conducted to examine shear characteristics and geometric variations, using four groups comprising 24 rough rock fractures. Subsequently, 360 non-Darcian flow experiments are performed to study the evolution of inertial and viscous permeability under cyclic shearing. It is observed that both types of permeability tend to decrease with an increasing number of shearing cycles. The most significant reduction occurs during the first cycle, followed by a slower decline that eventually stabilizes. A predictive model for non-Darcian flow is then developed, considering the geometry before shearing, rock properties, and cyclic shear characteristics. This model is validated against experimental data. Based on the proposed predictive model, a method for determining the critical number of shear cycles is also proposed. These findings contribute to understanding the evolution of non-Darcian flow in fractures subjected to seismic activity or repeated stress changes.