The applicability of four machine learning (ML) methods, ANFIS-PSO, ANFIS-FCM, MARS and M5Tree, together with multi model simple averaging (MM-SA) ensemble method, is investigated in rainfall-runoff modeling at hourly timescale. The results are compared with the conceptual EBA4SUB model using rainfall and runoff data from Samoggia River basin, Italy. The capability of the methods is measured using five statistics, Nash–Sutcliffe efficiency, root mean squared error, mean absolute error, scatter index, and adjusted index of agreement. Comparison of single ML reveals that the ANFIS-PSO, ANFIS-FCM and MARS produce similar accuracy which is better than the M5Tree model. MM-SA ensemble model improves the accuracy of ANFIS-PSO, ANFIS-FCM, MARS and M5Tree models with respect to RMSE by 8.5%, 5%, 7.4% and 28.8%, respectively. Comparison with the conceptual event-based method indicates that the ML methods generally performs superior to the EBA4SUB; however, latter method provides better accuracy than the M5Tree and MARS in some cases.