Improving student wellbeing and building resilience are crucial in preventing and reducing the impact of mental health problems. Schools play a vital role in promoting student wellbeing. However, there is little clear evidence about the effectiveness of school-based wellbeing programs in terms of their impact on both students’ wellbeing and on academic outcomes. Few systematic reviews consider academic outcomes, and previous reviews on wellbeing are narrow in scope. This document is the protocol for a systematic review which addresses these limitations, guided by the following research question: “How effective are school-based wellbeing interventions for improving the academic and non-academic outcomes of children and young people in mainstream schools?”