Schools start early in the morning all over the world, contrasting with adolescents’ late chronotype. Interestingly, lower academic performance (i.e. grades or qualifications) was associated with later chronotypes. However, it is unclear whether it is a direct effect of chronotype or because students attend school too early to perform at their best. Moreover, little is known about how this affects students’ academic success beyond their grades. To address this gap in knowledge, we studied how school timing and chronotype affect grade retention (i.e. repeat a year) in a unique sample of students randomly assigned to one of three different school timings (starting at 07:45, 12:40, or 17:20). Even when controlling for academic performance, we found that later chronotypes exhibit higher odds of grade retention only in the morning, but not in later school timings. Altogether, ensuring a better alignment between school timing and students’ biological rhythms might enhance future opportunities of adolescents.