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Ethiopia and South Sudan contain several population centers and important ecosystems that depend on July–August rainfall. Here we use two models to understand current and future rainfall: the first ever pan-African numerical model of climate change with explicit convection and a parameterized model that resembles a typical regional climate model at 4.5 and 25 km horizontal grid-spacing, respectively. The explicit convection and higher resolution of the first model offer a greatly improved representation of both the frequency and intensity of rainfall, when compared to the parametrized convection model. Furthermore, only this model has success in capturing the east–west propagation of rainfall over the full diurnal cycle. Enhanced low-level westerlies were found for extremely wet days, though this response was weaker in the explicit convection model. The increased orographic detail in the explicit model resulted in the splitting of the low-level Turkana Jet core into smaller cores, and inhibited its penetration far into South Sudan. Some projected changes were found to be independent of model, such as changes in the strength of Somali and Turkana jets, as well as the shifting of Turkana jet core to lower levels. However, the explicit model end-of-century projections showed a larger and clearer decrease in wet days, accompanied by an increase in wet day intensity and extreme rainfall. This study highlights serious limitations of relying solely on simulations which parameterize convection to inform decisions in the region of South Sudan and Ethiopia.