Abstract It is well known that the Indian Ocean dipole (IOD) and El Niño–Southern Oscillation (ENSO) are closely related to rainfall variability over East Africa. This study found that the preceding August–October (ASO) Southern Annular Mode (SAM) can influence East African rainfall from October to December [i.e., East African short rains (EASR)], with a strong and significant relationship during the period of 1992–2019 than 1971–91. This is likely a result of the changes in SAM variations. It is further revealed that, during 1992–2019, the ASO SAM, via air–sea interactions, can excite meridional dipole sea surface temperature anomalies (SSTA) and warm SSTA over the southern Indian and Atlantic Oceans, respectively. In contrast, during 1971–91, the SAM induces warm SSTA over the southern Indian Ocean. Further analysis indicated that these ASO SAM-related SSTA patterns persist through the following October–December and exert a contrasting influence on the EASR. Based on the possible mechanism, the enhanced influence of SAM on EASR appears to be achieved through significant meridional circulation in the Indian Ocean basin, with anomalous sinking motion in the extratropics and the rising motion in the tropical Maritime Continent (MC) region. Correspondingly, strong convection is enhanced over the MC, altering zonal vertical circulation. This process results in anomalous westerlies in the tropical Indian Ocean, which reduces the atmospheric moisture, weakens convection, and suppresses rainfall over the central-western Indian Ocean, including the study region. Further analysis suggests that the prediction skill of the EASR related to the SAM, ENSO, and IOD was enhanced during 1992–2019. Significance Statement Several studies have investigated the influence of tropical climate anomalies, such as El Niño–Southern Oscillation and the Indian Ocean dipole, on the rainfall variability over East Africa. The region continues to be plagued by numerous climate-related disasters, including flooding and drought, and the associated varying impacts have been detrimental. As such, there is a need to understand further the factors and associated physical processes that cause such events and improve forecasting accuracy. This research emphasizes the role of the Southern Annular Mode (SAM), finding a strengthened lagged relationship with East African rainfall in recent decades. This implies that changes in the SAM should be considered in understanding present and future rainfall variability in the region.