Women comprise close to half of the student body in many of the world’s leading universities. However, in Japan, only 1 in 4 students is a woman in the 7 elite national universities, which are the Japanese equivalent of the Ivy League. Since elite universities shape cultural and social norms, gender inequality in such institutions may reflect and reproduce gender inequality. Therefore, better understanding its causes is an important policy issue. The low female percentage is not because of any discriminatory policies taken by the universities. The reality is that women are also underrepresented in the applicant pool. Even within the same academic level, females are less likely to apply for elite universities than males. Why is this the case? I surveyed the Japanese high school students to examine what holds females back from applying for the elite national universities and found that low wage return to elite education perceived by female students is an important factor. The result shows that female students who want to work with higher intensity after marriage are more likely to apply for the elite national universities, but many female students do not want to live like that. My findings imply that this is because female students think it would be hard to balance high-intensity work and family duty after marriage. This demonstrates that actions within the education system alone may be insufficient to change the gender disparity in elite universities and broader social change would be necessary.