Calibration and uncertainty analysis is necessary to perform the best estimation and uncertainty identification of hydrological models. This paper uses the Soil and Water Assessment Tool-Calibration and Uncertainly Procedures (SWAT-CUP) model to analyze the uncertainty of SWAT model in a Japanese river catchment. The GLUE and SUFI-2 techniques used in this analysis show quite good results with high value of R2 as 0.98 and 0.95 for monthly simulation. Daily simulation results during calibration and validation are also good with R2 as 0.86 and 0.80. For uncertainty results, the 95% prediction uncertainty (95PPU) brackets very well with the observation. The p-factors of uncertainty analysis for the calibration and validation periods are 92% and 94%. The calibration result by using GLUE shows better than that by using SUFI-2. However, the processing time of the GLUE approach is longer than SUFI-2 approach when they were run in the SWAT-CUP. The uncertainty analysis indicates that the parameters of effective hydraulic conductivity in main channel alluvium (CH_K2) and base-flow alpha factor for bank storage (ALPHA_BNK) play important roles for calibration and validation of SWAT model.