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Sweet potato is in its introductory phase as a food-based approach to alleviate malnutrition in the Afar region, where, due to climate change, agricultural drought impedes crop production. This study assesses the impact of climate change on orange-fleshed sweet potato (OFSP) fresh storage root yield production over the Afar region using the Aqua Crop model. This model was fed with daily rainfall and minimum and maximum temperature datasets, for the baseline climate (1980–2009) as well as future (2010–2099) climate projections under two representative concentration pathways: RCP 4.5 and RCP 8.5. These datasets were statistically downscaled from twenty (20) general circulation models that are used in the Coupled Model Intercomparison Project Phase 5 (CMIP5). The impact of climate change on sweet potatoes was assessed by comparing the change in average sweet potato yields in the baseline climate condition against the average of simulated sweet potato yields in the Near-term (NT) (2010–2039), Mid-term (MT) (2040–2069), and End-term (ET) (2070–2099) under RCP 8.5 and RCP 4.5. Simulation shows increased future storage root yield production for NT (3.23%), MT (3.90%), and ET (7.25%) under RCP 4.5 and MT (5.88%) and NT (6.71%) from the observed yield data (32.0 t/ha) except for Near-term (−9.59%) under RCP 8.5. Similarly, projected climate shows increase in temperature Tmax (0.93–4.10 °C), Tmin (0.88–4.54 °C) and precipitation (28.9–37.8%) under both RCPs which will favor sweet potato yield production increase in near-term, mid-term reaching climax in end-term. Simulation with planting dates shows that normal planting date (July 01), gives better yields than early (April 22) or late planting (01 August). This finding may perhaps be used as preliminary data in adoption and upscaling of orange-fleshed sweet potato in Afar region.