Despite concerns raised on the inequality in healthcare provision in Japan, little is known about the factors that hinder candidates' application to medical schools. A nationwide cross-sectional survey was conducted to identify the impact of economic factors and living place on students' choice of and preparation for medical school. The survey was administered to high school teachers with career advisory roles, as they support and likely influence students' choice and decision on this matter. Responses totaling 1,094 were obtained from 1,746 high schools across Japan. The ratio of high schools with two or more students enrolled in medical schools every year is higher in private schools, those with high tuition, and those located in big cities. Approximately 66.8% of the respondents agreed that "It is difficult for students in economically disadvantaged families to enroll in medical schools;" 42.0% agreed that "Some students gave up on aspiring to enter medical schools because they could not afford it," and 61.2% agreed that "Students living in urban areas are more likely to enroll in medical schools." When asked about the percentage of students attending prep school among those aspiring for a medical career, significantly more respondents from private versus public high schools answered "80% or more." When asked about the percentage of parents who are doctors or dentists among students aspiring for a medical career, significantly more respondents from private versus public high schools answered "50% or more." The results suggest that students from lower-income families and those living in rural areas are more likely to be disadvantaged when choosing a medical career (because of financial difficulties) than those who live in urban areas and come from wealthier families. The results imply that economic and geographical divides in medical admission are reflected in high school teachers' perception of and support provided to students.