The hydrological conditions upstream of the Ciliwung watershed are changing due to climate and land-use changes. Any changes in this area may increase the flood frequencies which may have countless consequences downstream of the watershed where the Jakarta city is located. We simulated the effects of land-use and climate changes on flooding (e.g., peak flow and river discharge) in the upper Ciliwung River basin in Greater Jakarta, Indonesia. Hydrologic Modeling System (HEC-HMS), a rainfall-runoff simulation model, was used to simulate peak river discharge values for current and future conditions. The model was calibrated and validated based on the observed river discharge data from February 2007 and January 1996, respectively. The statistical analysis showed that the performance of the model is satisfactory, with Nash–Sutcliffe efficiency 0.64 and 0.58 for calibration and validation, respectively. The coefficients of determination values are 0.86 and 0.82, respectively. The effect of the projected land-use changes alone in 2030 increased the peak flow by approximately 20%. When considering the land-use changes in conjunction with the future climate scenario, the peak flow based on the precipitation corresponding to a 50-year return period in 2030 increased by 130%. Based on the results of this study, it is urgent that a flood management plan be implemented in the target area to reduce flooding in the near future.