Abstract Rainfall over the Horn of Africa (HoA) exhibits pronounced interannual variability linked to the El Niño‐Southern Oscillation (ENSO). However, the seasonal evolution of ENSO‐driven rainfall anomalies is not adequately explained by the ENSO, particularly the Niño3.4 index. The results here show that nonlinear interactions between ENSO and both semiannual and annual migration of the Intertropical Convergence Zone generate a combination mode (C‐Mode) that modulates the timing and amplitude of the HoA regional rainfall. The C‐Mode reproduces the rainfall variability during both the October‐November‐December and March‐April‐May rainy seasons, and captures statistically significant spectral peaks at combination frequencies near 1 and 2 years−1. Regression and reconstruction analyses indicate that the inclusion of the C‐Mode substantially improves representation of the bimodal rainfall response. These findings highlight the key role of ENSO–seasonal cycle in driving HoA rainfall variability and provide a physically‐based pathway for the region’s improved seasonal prediction.