Abstract: Although historical disputes have periodically upset Japan–South Korea relations for decades, the deterioration of ties after 2011 was unprecedented. Focusing on the string of events that led to the rapid bilateral downturn, this article analyses Japan’s changing strategic thinking on South Korea. It finds that Japanese policy-makers perceive a strong overlap in strategic interests with Seoul on two issues, namely the North Korean threat and the United States’ presence in Asia. However, both structural changes in the region—including China’s rise and shifts in the relative power between Japan and South Korea—and domestic developments are undermining Tokyo–Seoul relations. We identify three fault-lines that have opened up in the relationship and are compounding existing sources of friction: strategic, historical–psychological and economic fault-lines. The strategic fault-line in particular weighs heavily on ties, with Tokyo and Seoul diverging in their approaches to China. Trends in all three fault-lines have combined to foster mutual suspicion about intentions and strategic orientation. Overall, Japanese policy-makers feel that their capability to bring about a reset in relations with Seoul is limited. This creates a predicament for Tokyo, as it recognizes South Korea as a strategically important country, especially in facing North Korea.