Input selection for data-driven rainfall-runoff models is an important task as these models find the relationship between rainfall and runoff by direct mapping of inputs to output. In this study, two different input selection methods were used: cross-correlation analysis (CCA), and a combination of mutual information and cross-correlation analyses (MICCA). Selected inputs were used to develop adaptive network-based fuzzy inference system (ANFIS) in Sungai Kayu Ara basin, Selangor, Malaysia. The study catchment has 10 rainfall stations and one discharge station located at the outlet of the catchment. A total of 24 rainfall-runoff events (10-min interval) from 1996 to 2004 were selected from which 18 events were used for training and the remaining 6 were reserved for validating (testing) the models. The results of ANFIS models then were compared against the ones obtained by conceptual model HEC-HMS. The CCA and MICCA methods selected the rainfall inputs only from 2 (stations 1 and 5) and 3 (stations 1, 3, and 5) rainfall stations, respectively. ANFIS model developed based on MICCA inputs (ANFIS-MICCA) performed slightly better than the one developed based on CCA inputs (ANFIS-CCA). ANFIS-CCA and ANFIS-MICCA were able to perform comparably to HEC-HMS model where rainfall data of all 10 stations had been used; however, in peak estimation, ANFIS-MICCA was the best model. The sensitivity analysis on HEC-HMS was conducted by recalibrating the model by using the same selected rainfall stations for ANFIS. It was concluded that HEC-HMS model performance deteriorates if the number of rainfall stations reduces. In general, ANFIS was found to be a reliable alternative for HEC-HMS in cases whereby not all rainfall stations are functioning. This study showed that the selected stations have received the highest total rain and rainfall intensity (stations 3 and 5). Moreover, the contributing rainfall stations selected by CCA and MICCA were found to be located near the outlet of contributing sub-catchments. This provides valuable information towards identifying the more contributing sub-catchments in catchments such as Sungai Kayu Ara where no flow measurement is available for sub-catchments.