Absolute ability/achievement does not explain gender differences in educational trajectories, but the role of comparative advantage (i.e., being better in one subject compared to another) has received much less attention. To study this, longitudinal data collected among 1,352 individuals (age 15-16) in upper secondary education in the Netherlands are used. Multinomial path analyses showed that compared to girls, boys are on average 15% more likely to enter the most male-typical trajectory and 16% less likely to enter the most female-typical trajectory. Although having a comparative advantage affects trajectory choices, it does not explain gender differences in trajectory choices in secondary education.