This article elucidates the reasons behind South Korea’s diminished security cooperation with Japan during the Moon Jae-in administration (2017–2022). The author discovered that President Moon halted ongoing security cooperation activities initiated by his predecessor, even though the North Korean nuclear threat became exponential. In particular, this article argues that not the national-level factors, such as South Koreans’ negative perception of Japan on the basis of their collective memory, but the leader factor was the main reason for the worsening of South Korea–Japan’s security cooperation during the Moon administration, contrary to most people’s expectations. The Moon administration’s progressive political leaders, who had acquired anti-United States/anti-Japan and pro-North Korea/pro-China perspectives during their anti-government protests in the 1970s and 1980s, decided to be confrontational towards Japan to their political benefit. The reality that the security cooperation between South Korea and Japan jumpstarted once the conservative Yoon Suk-yeol administration leaders replaced them supports this finding.