As a common foundation material for railway subgrades, red mudstone is prone to fatigue damage and deformation under the impact of high-cycle train loads. To comprehensively understand the dynamic damage and deformation behaviour of soft red mudstone, high-cycle cyclic loading tests were carried out to investigate the deformation and crack evolution of soft red mudstone based on acoustic emission (AE) parameter analysis. Then, monotonic compression was performed, and the impact of self-healing on AE characteristics was studied. Tests results showed that cyclic loadings are more likely to cause the matrix loosening and produce small size micro-cracks compared with monotonic loadings. And AE signals exceeding 300 kHz of high frequency increases with the increase of loading frequency, indicating the size of micro-cracks decreases with the increase of loading frequency. The proportion of shear cracks increases exponentially with the increase of upper limit stress but decreases linearly with the increase of loading frequency. Kaiser effect of soft red mudstone decreases or even disappears under the effect of self-healing with the increase of the interval time Δt between cyclic and monotonic loads. In addition, it is found radial strain is more sensitive to the rock’s damage progression compared to axial strain. There is a stronger correlation between axial strain and the damage under cyclic loading conditions than under monotonic loading conditions. The volume strains of rock samples under cyclic loading are relatively smaller compared to monotonic loading under the same damage variable.