The proportion of women in Japanese higher education has gradually increased, but men still dominate in majors such as science and engineering. As a background to this gender segregation, some survey results show that even before entering high school, there is a tendency for boys to evaluate themselves as the "science type" and girls as the "humanities type." Based on these findings, this study focused on the humanities and science self-concepts of junior high school students and examined the mechanism of gender differentiation. Based on the multivariate analysis of the questionnaire survey, it was found that the extent to which gender differences in self-recognition of scientific ability and preference for science subjects explain gender differences in humanities and science self-concepts was limited, and it was confirmed that when students themselves or their parents believed gender stereotypes, girls were less likely to evaluate themselves as the "science type." These results indicate that factors other than students' academic abilities influence the reluctance of girls to evaluate themselves as the "science type." The findings of this study suggest the importance of neutralizing gender stereotypes present in Japanese society.