Schools start early in the morning all over the world, contrasting with adolescents’ late chronotype. These early school timings have negative consequences on academic performance (i.e. grades), which are worse for students with later chronotypes. This academic disadvantage has been associated with the misalignment between school schedule and adolescents’ internal timing, but it is unclear 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 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.