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Sex segregation in field of study is one of the key mechanisms to explain the unequal distribution of men and women in the labor market in Japan. By using publicly available administrative education statistics, this study investigates trends in sex segregation in the field of study from 1975 to 2019. We paid particular attention to (1) different trends in non-STEM, STEM, and health fields and (2) heterogeneity across national, public, and private institutions with different demands in higher education. We applied Duncan’s dissimilarity index to 68 fields of study among college students. Results show that sex segregation in field of study decreased dramatically over the 45 years by 43%, from 69 to 39. This is mainly driven by the massive integration of men and women in non-STEM fields in private institutions. Despite the overall declining trend, we also found that trends differ by institutional characteristics of universities and fields. In particular, declining trends in segregation are slow in recent years, especially at national and public institutions. These stalled trends are explained by (1) a slow decline in segregation in STEM fields and (2) a rise in segregation in health fields in public institutions. This study concludes to suggest that the slow integration of STEM fields may support the theory of stalled gender revolution in Japan and horizontal aspects of educational inequality may increase because of the growing demand for the workforce to deal with population aging in the future.