Accurate prediction of pan evaporation (PE) is one of the crucial factors in water resources management and planning in agriculture. In this research, two hybrid models, self-adaptive time-frequency methodology, ensemble empirical mode decomposition (EEMD) coupled with support vector machine (EEMD-SVM) and EEMD model tree (EEMD-MT), were employed to forecast monthly PE. The EEMD-SVM and EEMD-MT were compared with single SVM and MT models in forecasting monthly PE, measured between 1975 and 2008, at Siirt and Diyarbakir stations in Turkey. The results were evaluated using four assessment criteria, Nash–Sutcliffe Efficiency (NSE), root mean square error (RMSE), performance index (PI), Willmott's index (WI), and Legates–McCabe's index (LMI). The EEMD-MT model respectively improved the accuracy of MT by 36 and 44.7% with respect to NSE and WI in the testing stage for the Siirt station. For the Diyarbakir station, the improvements in results were less spectacular, with improvements in NSE (1.7%) and WI (2.2%), respectively, in the testing stage. The overall results indicate that the proposed pre-processing technique is very promising for complex time series forecasting and further studies incorporating this technique are recommended.