Amidst global concerns about land use change and its far-reaching impact on biodiversity and human well-being, there is a growing need to understand how land use stock and flow changes over time through land use accounting. While existing studies on land accounting have focused on historical land changes, little attention has been paid to future transitions. This study assessed historical patterns and projected future shifts in land use dynamics from 1987 to 2050 across Japan by combining high-resolution land use and land cover datasets, land change simulations, and land accounting. In the analyses, particular attention was paid to the historical and future trends of farmland abandonment by leveraging data at 100-m resolution built on national vegetation surveys. High-resolution analysis of farmland abandonment issue with national scale in Japan is a novelty. From 1987 to 1998, the land stock analysis results showed a pronounced marked increase in residential land (10.4%) and grassland (16.9%); the flow analysis results showed that urban residential sprawl expansion was mainly formed by secondary (32.6%) and plantation (21.1%) forest areas, coinciding with increasing population and economic growth. Projections from 2010 to 2050 indicate a marked increase in abandoned farmland (67.2% per decade), a trend influenced by rapid population decline and presumably agricultural policies, especially significant in regions such as Hokkaido and Kyushu. The findings of this study are crucial for shaping policy and decision-making, underlining the need for sustainable land management strategies that effectively balance urban growth, agricultural productivity, and environmental preservation in Japan.