BACKGROUND: Research investigating the effectiveness of universal interventions to reduce the risk of mental health problems remains limited. Schools are a promising setting within which adolescents can receive interventions aimed at promoting their mental health. The aim of this study is to assess the effectiveness of a resilience-based prevention-focused intervention in reducing the risk of mental health problems among adolescents attending secondary school in socio-economically disadvantaged areas. METHODS/DESIGN: A cluster randomised control trial will be conducted, with schools as the unit of randomisation. Initially, 32 secondary schools will be randomly allocated to a control or intervention group (12 control and 20 intervention). An intervention focused on improving student internal and external resilience factors will be implemented in intervention schools. A survey of students in Grade 7 in both intervention and control schools will be conducted (baseline) and repeated three years later when the students are in Grade 10. The Strengths and Difficulties Questionnaire will be used to measure the risk of mental health problems. At follow-up, the risk of mental health problems will be compared between Grade 10 students in intervention and control schools to determine intervention effectiveness. DISCUSSION: The study presents an opportunity to determine the effectiveness of a comprehensive resilience-based intervention in reducing the risk of mental health problems in adolescents attending secondary schools. The outcomes of the trial are of importance to youth, schools, mental health clinicians and policymakers. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry, ACTRN12611000606987, registered 14 June 2011.