This study aimed at application of SWAT model for hydrological simulations of Rapti River Basin (RRB) water systems. The Rapti River originates from Nepal and then it comes in India. SWAT (Soil and Water Assessment Tool) model was used for hydrological simulation of the RRB surface and sub surface water systems. SWAT is a comprehensive, semi-distributed river basin model that requires a large number of input parameters, which complicates model parameterization and calibration. The RRB was discretised into 4 sub-basins and 630 hydrological response units (HRUs) and calibration and validation was carried out at Bagasoti using monthly flow data of 11 years, respectively. We first calibrated the model in SWAT-CUP which is a decision-making framework that incorporates a semi-automated approach (SUFI2) using manual calibration and incorporating sensitivity and uncertainty analysis. Parameter sensitivity analysis helps focus the calibration and uncertainty analysis and is used to provide statistics for goodness-of-fit. In this study Calibration has been done between simulated and observed discharge data (1974-1985) for 50 simulations with 6 parameters that is Curve number (CN2 = 0.945), Groundwater delay (GW_DELAY = 50), Baseflow alpha factor (ALPHA_BF = 0.58), Manning's "n" value for the main channel (CH_N2 = 0.15), Effective hydraulic conductivity in main channel alluvium (CH_K2 = 10.20) and Available water capacity of the soil layer (SOL_AWC = 0.28). The results were analysed and compared with the observational data. The model performance evaluation showed acceptable ranges of values (i.e., Nash Sutcliff was 0.75 and R2 was 0.71). After model calibration, in order to predict water balance, the model was validated by using the best parameter.