Jakarta is facing several issues related to flooding, includ­ing land subsidence in the coastal area and rapid land-use/cover changes in the upstream area. In this study, we analyzed the effects of future changes in land use and land subsidence using a rainfall-runoff and flood inundation model. The future land-use scenarios were projected based on the SLEUTH model, and land subsidence was projected based on an extrapolation of the current state in Jakarta. Based on this analysis, land-use changes and land subsidence contributed to an increase in flood inundation volume of 36.8% from 2013 to 2050. Moreover, the effects of land-use changes on flood inundation in Jakarta were much greater than those of land subsidence. The government’s current target to stop land subsidence by 2020 would cause a 7.7% decrease in the flood inundation volume by 2050. Furthermore, controlling and regulating land-use/cover changes by 2020 would cause a 10.9% decrease in the flood inundation volume by 2050. From these results, we conclude that a flood mitigation plan should be made not only for land subsidence, but also for land-use changes.