Abstract Under cyclic loading, rock joints underwent 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, numerical simulations of rough joints under cyclic shear stress, involving variations in normal stiffness, loading amplitudes, and loading frequencies, were performed using a cyclic shear loading method based on the FISH language. The results indicated that there was a hysteretic effect in the shear stress–shear displacement curves of joints. During cyclic shear stress, the shear velocity of the joint fluctuated from positive to negative, with the maximum shear velocity changing by approximately 10 times, increasing from 0.012 × 10–2 to 0.15 × 10–2 mm/s before and after joint instability. As normal stiffness increased to the same shear displacement, more cracks developed in the joint. When the normal stiffness exceeded 3 GPa/m, a conspicuous failure zone was evident. Loading amplitude showed an inverse proportionality to the number of cycles required to achieve the target shear displacement. Loading frequency exhibited a linear proportionality to the number of cycles needed to reach the target shear displacement The fatigue damage degree of joints during cyclic shear could be represented by two indices: the Felicity ratio (FR) and the damage variable (D). Under different conditions, the critical D value ranged from 0.037 to 0.097, while the corresponding critical FR value varied between 0.700 and 0.822, reflecting the impact of normal stiffness, amplitude, and frequency on joint fatigue failure.