The gender gap in college major choice has become an important issue in higher education. In particular, female students are underrepresented in natural science majors in many countries. This paper estimates students’ preference for college majors, in addition to other attributes of college education programs. We use a fully randomized conjoint survey experiment, which allows us to estimate preference for each program attributes, including tuition fees, labor market conditions after graduation, gender composition within the university and the department, and college major. We find a large gender gap in the preference for college major even when other attributes are held constant. The female respondents do not prefer natural science majors, on average. The heterogeneity analysis also shows consistent results: a positive preference for natural science majors is not observed even in female respondents with high math grades in junior high school.