The estimation of reference evapotranspiration (ETo), a crucial step in the hydrologic cycle, is essential for system design and management, including the balancing, planning, and scheduling of agricultural water supply and water resources. When climates vary from arid to semi-arid, and there are problems with a lack of meteorological data and a lack of future information on ETo, as is the case in Egypt, it is more important to estimate ETo precisely. To address this, the current study aimed to model ETo for Egypt’s most important agricultural governorates (Al Buhayrah, Alexandria, Ismailiyah, and Minufiyah) using four machine learning (ML) algorithms: linear regression (LR), random subspace (RSS), additive regression (AR), and reduced error pruning tree (REPTree). The Climate Forecast System Reanalysis (CFSR) of the National Centers for Environmental Prediction (NCEP) was used to gather daily climate data variables from 1979 to 2014. The datasets were split into two sections: the training phase, i.e., 1979–2006, and the testing phase, i.e., 2007–2014. Maximum temperature (Tmax), minimum temperature (Tmin), and solar radiation (SR) were found to be the three input variables that had the most influence on the outcome of subset regression and sensitivity analysis. A comparative analysis of ML models revealed that REPTree outperformed competitors by achieving the best values for various performance matrices during the training and testing phases. The study’s novelty lies in the use of REPTree to estimate and predict ETo, as this algorithm has not been commonly used for this purpose. Given the sparse attempts to use this model for such research, the remarkable accuracy of the REPTree model in predicting ETo highlighted the rarity of this study. In order to combat the effects of aridity through better water resource management, the study also cautions Egypt’s authorities to concentrate their policymaking on climate adaptation.