Floods are considered to be one of the major natural disasters in Indonesia. Jakarta in Indonesia has experienced many floods in the past, such as those in 1996, 2002, 2007 and 2013. In this paper, land subsidence problems contributing to flooding in Jakarta were described and historical and future land subsidence situations in Jakarta were reconstructed and projected using a simple linear extrapolation method. Also, those land subsidence impacts were analyzed by using a flood inundation model. As a result of analysis, it was found that the land subsidence in Jakarta contributed by 17.6% to increase of the total flood inundation volume from 1983 to 2013. Also, it was estimated that the land subsidence situations for the future period of 2050 would increase the flood inundation volume by 10.3% compared to those of 2013. However, impacts from land use/cover changes on the flood inundation were found to be much greater than those from land subsidence in Jakarta. It should be noted that the land subsidence affects flooding from the coast when high waves and surges occur but those effects were not considered in this paper.