This study constructs and estimates a structural equilibrium model of the medical school market in which students strategically apply to schools, and admission probabilities at specific institutions are endogenously determined. It empirically analyzes how gender differences in preferences related to distance from home impact gender disparities in public medical school admissions in Japan. Our results indicate that females incur greater costs associated with distance compared to males. While financial aid to offset distance-related costs can increase the proportion of female applicants to medical schools, it does not lead to a corresponding increase in female admissions due to the effects of competition. We propose a financially feasible alternative affirmative action policy that provides financial aid exclusively to female students to reduce the gender gap.