Understanding the fatigue failure mechanisms in concrete is complex and remains an area of ongoing investigation. Material heterogeneity, along with the size effect, plays a significant role in specifying the crack propagation behaviour and fatigue life in case of repetitive loading conditions. In this study, the influence of material heterogeneity on the fatigue behaviour of concrete has been examined. Three different-size beam specimens with varying heterogeneity (aggregate sizes) have been considered to investigate various fracture characteristics under repetitive load conditions. Acoustic emission and digital image correlation techniques have been employed to analyse crack growth behaviour. The results revealed that stiffness degradation and crack propagation rates are faster for the specimens with smaller aggregate sizes compared to the larger aggregate size specimens of the same depth. Moreover, the fatigue life and effective crack length at failure are also higher in the case of larger aggregate sizes compared to smaller ones. Therefore, a heterogeneity-adjusted, analytical model of fatigue crack growth has been proposed. Further, the AE parameters have been utilized to characterize the tensile and shear crack dominance in different stages of fatigue crack propagation. The outcome of this study can be utilized to anticipate the crack propagation behaviour and residual fatigue life for any combination of specimen size and aggregate size.