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Abstract Background Anxiety and depressive disorders typically emerge in adolescence and can be chronic and disabling if not identified and treated early. School-based universal mental health screening may identify young people in need of mental health support and facilitate access to treatment. However, few studies have assessed the potential harms of this approach. This paper examines some of the potential mental health-related harms associated with the universal screening of anxiety and depression administered in Australian secondary schools. Methods A total of 1802 adolescent students from 22 secondary schools in New South Wales, Australia, were cluster randomised (at the school level) to receive either an intensive screening procedure (intervention) or a light touch screening procedure (control). Participants in the intensive screening condition received supervised self-report web-based screening questionnaires for anxiety, depression and suicidality with the follow-up care matched to their symptom severity. Participants in the light touch condition received unsupervised web-based screening for anxiety and depression only, followed by generalised advice on help-seeking. No other care was provided in this condition. Study outcomes included the increased risk of anxiety, depression, psychological distress, decreased risk of help-seeking, increased risk of mental health stigma, determined from measures assessed at baseline, 6 weeks post-baseline, and 12 weeks post-baseline. Differences between groups were analysed using mixed effect models. Results Participants in the intensive screening group were not adversely affected when compared to the light touch screening condition across a range of potential harms. Rather, participants in the intensive screening group were found to have a decreased risk of inhibited help-seeking behaviour compared to the light touch screening condition. Conclusions The intensive screening procedure did not appear to adversely impact adolescents’ mental health relative to the light touch procedure. Future studies should examine other school-based approaches that may be more effective and efficient than universal screening for reducing mental health burden among students. Trial registration Australian and New Zealand Clinical Trials Registry (ACTRN12618001539224) https://anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375821 .