An application of a flood risk analysis system is presented for the analysis on the impact of a proposed flood control plan in the Ichinomiya river basin, Chiba Prefecture, Japan. The system consists of two main modules: a physically based distributed hydrological model for flood inundation and a geographical information system (GIS)-based raster model for flood loss estimation. In the system, the grid-based distributed hydrological model simulates surface flood inundation parameters for user-specified spatial and temporal resolutions. At the end of each time step the simulated flood parameters in each grid are transferred to the GIS-based model for economic loss estimation. The proposed flood control plan consisted of three structural measures. These measures were then incorporated into the system to analyze their impacts on the reduction of flood inundation and resulting economic impacts for 50-year and 100-year return-period rainfall scenarios in the basin. From the analyses, it was found that the proposed flood control plan can reduce flood inundation in the basin for 50-year and 100-year return-period rainfalls to a great extent, and the resulting urban and agriculture damage in the basin can be reduced by over 70%.