This study investigates competing explanations for the effect of education on native adolescents’ Muslim population size perceptions. Drawing on theories about heuristic reasoning, we analyze to what extent the effect of education on size perceptions may be explained by differences in contact with and prejudice towards Muslims. The hypotheses are tested using longitudinal data on adolescents in the Netherlands (N = 1218). Overall, there is a tendency to overestimate the size of the national Muslim population. Furthermore, we find that higher educated adolescents tend to provide lower estimates of the Muslim population size. This relationship is partially mediated by earlier differences in school composition, as Muslims are concentrated to a greater extent in lower education. The relation between education and size perceptions cannot be attributed to differences in prejudice. Hence, we conclude that the effect of education on size perceptions is likely due to greater numeracy rather than negative evaluations of the outgroup.