Background Depression frequently first emerges during adolescence, and one in five young people will experience an episode of depression by the age of 18 years. Despite advances in treatment, there has been limited progress in addressing the burden at a population level. Accordingly, there has been growing interest in prevention approaches as an additional pathway to address depression. Depression can be prevented using evidence-based psychological programs. However, barriers to implementing and accessing these programs remain, typically reflecting a requirement for delivery by clinical experts and high associated delivery costs. Digital technologies, specifically smartphones, are now considered a key strategy to overcome the barriers inhibiting access to mental health programs. The Future Proofing Study is a large-scale school-based trial investigating whether Cognitive Behaviour Therapies (CBT) delivered by smartphone application can prevent depression.Methods A randomized controlled trial targeting up to 20,000 Year 8 Australian secondary school students will be conducted. In Stage I, schools will be randomized at the cluster level to receive either the CBT intervention app (SPARX) or to a non-active control group comparator. The primary outcome will be symptoms of depression and secondary outcomes include psychological distress, anxiety and insomnia. At the 12-month follow-up, participants in the intervention arm with elevated depressive symptoms will participate in an individual-level RCT (Stage II) and be randomised to receive a second CBT app which targets sleep difficulties (Sleep Ninja) or a control condition. Assessments will occur at post-intervention (both trial stages), and at 6, 12, 24, 36, 48- and 60-months post-baseline. Primary analyses will use an intention-to-treat approach and compare changes in symptoms from baseline to follow-up relative to the control group using mixed effect models.Discussion This is the first trial testing the effectiveness of smartphone apps delivered to school students to prevent depression at scale. Results from this trial will provide much needed insight into the feasibility of this approach. They stand to inform policy and commission decisions concerning if and how such programs should be deployed in school-based settings in Australia and beyond.