OBJECTIVE To determine the longitudinal associations between perceived pubertal timing and recent substance use between the ages of 11 and 17 years. METHODS A school-based cohort sequential study of adolescents in rural North Carolina, USA (n = 6892, 50% female) in the 6-8th grades at baseline and interviewed across five consecutive semesters. METHODS Self-administered questionnaires in a group setting measured perceived pubertal development using the Pubertal Development Scale and adolescents reported past 3-month use of cigarettes, alcohol and marijuana. Latent class growth analysis determined the longitudinal relationships between perceived pubertal timing (early, on-time and late) and use of the three substances. RESULTS A negative quadratic model was the best-fitting model for all three substances. Higher proportions of early developers had used cigarettes and marijuana within the past 3 months at age 11 compared with on-time (P < 0.001 and P = 0.013) and late developers (P = 0.010 and P = 0.014) and a higher proportion of early developers had recently used alcohol at age 11 compared with on-time adolescents (P < 0.001). However, the proportion of recent cigarette and marijuana users increased more across adolescence for on-time adolescents compared with early developers (P = 0.020 and P = 0.037). Desistance in the proportion of substance users was similar for all adolescents (all P > 0.050). CONCLUSIONS Adolescents who believe they are more advanced in puberty than their peers are more likely to have used cigarettes, alcohol and marijuana recently compared with adolescents who believe they are on-time or late developing; these findings are mainly due to differences in use at age 11.