A Soil and Water Assessment Tool (SWAT) model was used to model streamflow in a tropical humid basin in the Cerrado biome, southeastern Brazil. This study was undertaken in the Upper São Francisco River basin, because this basin requires effective management of water resources in drought and high-flow periods. The SWAT model was calibrated for the period of 1978–1998 and validated for 1999–2007. To assess the model calibration and uncertainty, four indices were used: (a) coefficient of determination (R2); (b) Nash–Sutcliffe efficiency (NS); (c) p-factor, the percentage of data bracketed by the 95% prediction uncertainty (95PPU); and (d) r-factor, the ratio of average thickness of the 95PPU band to the standard deviation of the corresponding measured variable. In this paper, average monthly streamflow from three gauges (Porto das Andorinhas, Pari and Ponte da Taquara) were used. The results indicated that the R2 values were 0.73, 0.80 and 0.76 and that the NS values were 0.68, 0.79 and 0.73, respectively, during the calibration. The validation also indicated an acceptable performance with R2 = 0.80, 0.76, 0.60 and NS = 0.61, 0.64 and 0.58, respectively. This study demonstrates that the SWAT model provides a satisfactory tool to assess basin streamflow and management in Brazil.