The study evaluated nine empirical methods for estimating reference evapotranspiration (ETo) in Bosnia and Herzegovina (BiH) across different climatic zones. The methods compared were the Hargreaves–Samani method (HS), the modified Hargreaves–Samani method (HM), the calibrated Hargreaves–Samani method (HC), the Priestley–Taylor method (PT), the Copais method (COP), the Makkink method (MAK), the Penman–Monteith method based on air temperature and overall average windspeed (PMT2), the Penman–Monteith method based on air temperature and regional average windspeed (PMT1.3), and the Penman–Monteith method based on air temperature and site-specific windspeed (PMTlok). These methods were tested against the “Food Agricultural Organization-Penman Monteith approach” (FAO-PM). The evaluation was performed using data from 20 meteorological stations in BiH, considering a common irrigation season (April–October) for two periods (2000–2005 and 2018–2022). The stations represented three climatic zones: semi-arid (SA), dry sub-humid (DSH), and moist sub-humid (MSH). The performance and ranking of the ETo methods were analyzed using the TOPSIS method. The trend of ETo during the common irrigation season for the period from 2018 to 2022 was determined using the Mann–Kendall test. The results of the study indicated that the HC method showed the best performance across all three climatic zones. The average root mean square error (RMSE) was 0.67 mm day−1, 0.49 mm day−1, and 0.50 mm day−1 for the SA, DSH, and MSH zones, respectively. As an alternative to the HC method, the PT method is recommended for its favorable results in both periods and in all zones. On the other hand, the HS method exhibited the highest average overestimation, particularly in the MSH zone, where ETo values were 18% higher compared with those of the FAO-PM method. The COP method also showed high overestimation and was not recommended for use. Regarding the MAK method, it resulted in underestimation during the period from 2000 to 2005, ranging from 17% in the DSH zone to 11% in the MSH zone. However, its performance improved during the period from 2018 to 2022, for which it ranked second place in the MSH zone. Among the PMT methods, the PMTlok, which utilized local average windspeed, yielded the best results. Despite performing well in the neighboring country of Serbia, the HM method showed poor overall performance in BiH. The findings of this study can serve as a foundation for further research in BiH to enhance irrigation practices in response to climate changes.