This chapter evaluates the economic impacts of sea level rise on Japan’s 47 prefectures using a computable general equilibrium (CGE) model, focusing on the direct and indirect effects of land loss. By analyzing two future scenarios—SSP1-2.6, which assumes a sustainable socioeconomic pathway, and SSP5-8.5, which represents high greenhouse gas concentrations—the study examines how the loss of agricultural and developed land affects regional economies. The findings indicate that sea level rise could reduce Japan’s real GDP by 3.6% to 4.1% by 2100, with Saga, Aichi, and Tokyo among the most severely impacted regions. While the direct effects of land loss are significant, the analysis also emphasizes the importance of indirect effects, such as disruptions to supply chains and diminished interregional trade, which play a crucial role in shaping regional outcomes. Interestingly, some prefectures without direct land loss may experience economic gains as production demands shift from affected areas. The study highlights the need to consider both the negative and positive indirect effects across regions.