This study examines the effects of 1.5 °C and 2 °C global warming levels (GWLs) on intra-seasonal rainfall characteristics over the Greater Horn of Africa. The impacts are analysed based on the outputs of a 25-member regional multi-model ensemble from the Coordinated Regional Climate Downscaling Experiment project. The regional climate models were driven by Coupled Model Intercomparison Project Phase 5 Global Climate Models for historical and future (RCP8.5) periods. We analyse the three major seasons over the region, namely March-May, June-September, and October-December. Results indicate widespread robust changes in the mean intra-seasonal rainfall characteristics at 1.5 °C and 2 °C GWLs especially for the June-September and October-December seasons. The March-May season is projected to shift for both GWL scenarios with the season starting and ending early. During the June-September season, there is a robust indication of delayed onset, reduction in consecutive wet days and shortening of the length of rainy season over parts of the northern sector under 2 °C GWL. During the October-December season, the region is projected to have late-onset, delayed cessation, reduced consecutive wet days and a longer season over most of the equatorial region under the 2 °C GWL. These results indicate that it is crucial to limit the GWL to below 1.5 °C as the differences between the 1.5 °C and 2 °C GWLs in some cases exacerbates changes in the intra-seasonal rainfall characteristics over the Greater Horn of Africa.