There is much evidence to suggest that the gender wage gap in Japan is one of the highest in rich countries, while gender inequality in education at the vertical level is becoming increasingly equalized. A small number of studies suggest that the remaining gender gap can be attributed to horizontal segregation with respect to field of study, particularly female underrepresentation in STEM fields, and little is known about trends in sex segregation by field in Japan specifically. By using publicly available education statistics, the current study investigates these trends from 1975 through 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. The results of applying Duncan’s dissimilarity index to 68 fields of study among four-year university students reveal that the overall trend in sex segregation in field of study has decreased over the 45 years by 43%. We also found that trends differ based on both institutional characteristics of universities and academic field, as the declining segregation trend is mainly driven by the massive integration of men and women in non-STEM fields in private institutions. The declining trend in segregation has been slow in recent years, especially at national and public institutions. We explored potential mechanisms for these stalling trends, and suggest that the driving forces are (1) a slower integration of women in STEM fields and (2) a rise in segregation in health fields. These results provide support for the theory of a stalled gender revolution in Japan. This study concludes that the desegregation may not be linked to the gender equality in the labor market, and that horizontal segregation may even increase because of the growing demand for the workforce to deal with population aging in the future.