The 2018 Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT) survey revealed discrimination against women in the admissions process of four Japanese medical schools, although it is not known how unusual the trend is for entire medical schools to enroll men and women. Therefore, this paper aims to examine how women are disadvantaged when they take entrance examinations for medical schools in Japan, compared to other academic disciplines. A null hypothesis that the average enrollment rates by gender in each academic discipline from 2015 to 2020 are the same was used to test the population ratio, and p-values were calculated. The results showed that no significant gender differences were found in the other disciplines, but the male enrollment rate was significantly higher only in medical schools (p < 0.01). This could be because the academic performance of men exceeds that of women in admissions. However, the percentage of women who passed the national examination for medical practitioners has been consistently high since 1997, suggesting that women were subjected to more difficult admission standards than their male counterparts or may have performed better during their years at medical school. As university entrance examinations in Japan are conducted in a closed environment, further information is expected to be disclosed as the matter continues to attract social attention for a better admission system.