SummaryThe discrepancy in sleep timing between weekdays and weekends – social jetlag (SJL) – is known to negatively affect student quality of life (QOL). However, the association between social jetlag and physical/mental QOL among adolescents and the precise effect of social jetlag on depressive symptoms and daytime sleepiness remains unknown. This study investigated the longitudinal course, risk factors, and effects of social jetlag, a circadian misalignment, in a school‐based cohort. The participants were 427 students (13.3 ± 0.6 years, 45.2% girls) from five junior high schools. We performed a baseline survey in 2019 and a 1‐year follow‐up survey in 2020. Depressive symptoms, QOL, and daytime sleepiness were assessed using the Birleson Depression Self‐Rating Scale for Children, Paediatric Quality of Life Inventory, and Paediatric Daytime Sleepiness Scale. In the baseline survey, 49.6% of the students reported SJL ≥1 h, and 17.1% reported SJL ≥2 h. Among them, 37.2% and 6.8% reported persistent SJL at follow‐up, respectively. New incidences of SJL ≥1 h were associated with older age, non‐attainment of menarche or voice changes, and longer duration of smartphone use, whereas its persistence was associated with a later chronotype. Persistence of SJL ≥1 h and ≥2 h predicted depressive symptoms and daytime sleepiness at follow‐up, whereas new incidences of SJL ≥2 h predicted lower QOL. In conclusion, social jetlag has a persistent course, and daytime functioning can deteriorate as social jetlag becomes chronic. Our findings suggest the need for intensive interventions for social jetlag among adolescents.