Under cyclic loading, rock joints undergo continuous slipping and closure, resulting in fatigue damage to the joints and thereby affecting the stability of rock engineering projects. To investigate the fatigue shear characteristics of joints under cyclic stress, a series of laboratory shear tests were conducted. Subsequently, a numerical simulation of rough joints under cyclic shear stress, involving variations in normal stiffness, loading amplitudes, and loading frequencies, was performed using a cyclic shear loading method based on the FISH language. The results indicate that there is a hysteretic effect in the shear stress-shear displacement curves of joints. The hysteresis loop is initially small and densely distributed, expanding and becoming loosely distributed in the later stages of cyclic shear. During cyclic shear stress, the shear velocity of the joint fluctuates from positive to negative, with the maximum shear velocity changing more than 10 times before and after joint instability. As normal stiffness increases to the same shear displacement, more cracks develop in the joint. When the normal stiffness exceeds 3 GPa/m, a conspicuous failure zone is evident. Loading amplitude shows an inverse proportionality to the number of cycles required to achieve the target shear displacement. Loading frequency exhibits a linear proportionality to the number of cycles needed to reach the target shear displacement. The fatigue damage degree of joints during cyclic shear can be represented by two indices: FR value and D value. In this study, the critical D value for joints under all working conditions ranges from approximately 0.037 to 0.097, with the corresponding critical FR value ranging from about 0.700 to 0.822.