Studies of adults and adolescents suggest subjective socio-economic status (SES) is associated with health/well-being even after adjustment for objective SES. In adolescence, objective SES may have weaker relationships with health/well-being than at other life stages; school-based social status may be of greater relevance. We investigated the associations which objective SES (residential deprivation and family affluence), subjective SES and three school-based subjective social status dimensions (“SSS-peer”, “SSS-scholastic” and “SSS-sports”) had with physical symptoms, psychological distress and anger among 2503 Scottish 13–15 year-olds. Associations between objective SES and health/well-being were weak and inconsistent. Lower subjective SES was associated with increased physical symptoms and psychological distress, lower SSS-peer with increased psychological distress but reduced anger, lower SSS-scholastic with increased physical symptoms, psychological distress and anger, and lower SSS-sports with increased physical symptoms and psychological distress. Associations did not differ by gender. Objective and subjective SES had weaker associations with health/well-being than did school-based SSS dimensions. These findings underline the importance of school-based SSS in adolescence, and the need for future studies to include a range of school-based SSS dimensions and several health/well-being measures. They also highlight the need for a focus on school-based social status among those working to promote adolescent health/well-being. •We examined associations between adolescent social status and several health measures.•Models included objective and subjective socio-economic status and school peer, scholastic and sports status.•School status had stronger associations with health than did socio-economic status.•Different school status dimensions and health measures were associated in different ways.•Studies should include a range of school status dimensions and health measures.