Sustainable management and informed policy making at the sub-national level requires an understanding of regional resource base regeneration and the demand it places on wider geographical areas. Ecological Footprint is one of the most widely used and accepted ecological accounting methodologies and available for calculating multiple consumption categories such as food, housing and transportation. Japan's 47 prefectures are diverse in their urbanization and ageing situations and provide an opportunity for understanding the relationship between regional socioeconomic and demographic factors and Ecological Footprint outcomes. To assess potential environmental impacts and planning implications of future urbanization and ageing, we analyzed the existing relationships between the proportion of urban and elderly populations and incomes, and the total and categorical Ecological Footprint per capita. We used a standard top-down scaling methodology to quantify the Ecological Footprint of prefectures, that included three steps: 1) acquiring national level data of Ecological Footprints, 2) applying environmental extended multi-regional input-output model to derive Ecological Footprint values by economic sector, and 3) scaling down Ecological Footprints to the prefecture level with household expenditure survey and other data sources. We show that Ecological Footprint per capita varies considerable among prefectures, being highest in Tokyo (5.24 global hectare) and lowest in Yamanashi (4.06 global hectare). Prefectures with a higher proportion of urban and elderly population had high total and food Ecological Footprint per capita. Prefectures with higher income per capita also had higher total and food Ecological Footprint per capita. Lower Ecological Footprints of less urbanized prefectures provide an argument for economic decentralization. Policy makers in ageing regions should consider supporting local food activities with elderly populations, as processed food dominates majority part of the food Ecological Footprint.