Most adolescents exhibit very late chronotypes and attend school early in the morning, a misalignment that can affect their health and psychological well-being. Here we examine how the interaction between the chronotype and school timing of an individual influences academic performance, studying a unique sample of 753 Argentinian students who were randomly assigned to start school in the morning (07:45), afternoon (12:40) or evening (17:20). Although chronotypes tend to align partially with class time, this effect is insufficient to fully account for the differences with school start time. We show that (1) for morning-attending students, early chronotypes perform better than late chronotypes in all school subjects, an effect that is largest for maths; (2) this effect vanishes for students who attend school in the afternoon; and (3) late chronotypes benefit from evening classes. Together, these results demonstrate that academic performance is improved when school times are better aligned with the biological rhythms of adolescents. Most adolescents exhibit late chronotypes but attend school early in the morning. Goldin et al. show that sleep is longer and academic performance is improved when school time is better aligned with the biological rhythms of students.