Background Suicide is the leading cause of death among young Australians, accounting for one-third of all deaths in those under 25. Schools are a logical setting for youth suicide prevention activities, with universal, selective and indicated approaches all demonstrating efficacy. Given that international best practice recommends suicide prevention programmes combine these approaches, and that to date this has not been done in school settings, this study aims to evaluate a suicide prevention programme incorporating universal, selective and indicated components in schools. Methods This study is a trial of a multimodal suicide prevention programme for young people. The programme involves delivering universal psychoeducation (safeTALK) to all students, screening them for suicide risk, and delivering internet-based Cognitive Behavioural Therapy (Reframe IT) to those students identified as being at high risk for suicide. The programme will be trialled in secondary schools in Melbourne, Australia, and target year 10 students (15 and 16 year-olds). safeTALK and screening will be evaluated using a single group pre-test/post-test case series, and Reframe IT will be evaluated in a Randomised Controlled Trial. The primary outcome is change in suicidal ideation; other outcomes include help-seeking behaviour and intentions, and suicide knowledge and stigma. The programme’s cost-effectiveness will also be evaluated. Discussion This study is the first to evaluate a suicide prevention programme comprising universal, selective and indicated components in Australian schools. If the programme is found to be efficacious and cost-effective, it could be more widely disseminated in schools and may ultimately lead to reduced rates of suicide and suicidal behaviour in school students across the region.