This study aimed to evaluate the impact of climate change on flood damage and the effects of mitigation measures and combinations of multiple adaptation measures in reducing flood damage. The inundation depth was calculated using a two-dimensional unsteady flow model. The flood damage cost was estimated from the unit evaluation value set for each land use and prefectures and the calculated inundation depth distribution. To estimate the flood damage in the near future and the late twenty-first century, five global climate models were used. These models provided daily precipitation, and the change of the extreme precipitation was calculated. In addition to the assessment of the impacts of climate change, certain adaptation measures (land-use control, piloti building, and improvement of flood control level) were discussed, and their effects on flood damage cost reduction were evaluated. In the case of the representative concentration pathway (RCP) 8.5 scenario, the damage cost in the late twenty-first century will increase to 57% of that in the late twentieth century. However, if mitigation measures were to be undertaken according to RCP2.6 standards, the increase of the flood damage cost will stop, and the increase of the flood damage cost will be 28% of that in the late twentieth century. By implementing adaptation measures in combination rather than individually, it is possible to keep the damage cost in the future period even below that in the late twentieth century. By implementing both mitigation and adaptation measures, it is possible to reduce the flood damage cost in the late twenty-first century to 69% of that in the late twentieth century.