INTRODUCTION: The first years of school are critical in establishing a foundation for positive long-term academic, social and well-being outcomes. Mindfulness-based interventions may help students transition well into school, but few robust studies have been conducted in this age group. We aim to determine whether compared with controls, children who receive a mindfulness intervention within the first years of primary school have better: (1) immediate attention/short-term memory at 18 months post-randomisation (primary outcome); (2) inhibition, working memory and cognitive flexibility at 18 months post-randomisation; (3) socio-emotional well-being, emotion-regulation and mental health-related behaviours at 6 and 18 months post-randomisation; (4) sustained changes in teacher practice and classroom interactions at 18 months post-randomisation. Furthermore, we aim to determine whether the implementation predicts the efficacy of the intervention, and the cost effectiveness relative to outcomes. METHODS AND ANALYSIS: This cluster randomised controlled trial will be conducted in 22 primary schools in disadvantaged areas of Melbourne, Australia. 826 students in the first year of primary school will be recruited to detect between groups differences of Cohen's d=0.25 at the 18-month follow-up. Parent, teacher and child-assessment measures of child attention, emotion-regulation, executive functioning, socio-emotional well-being, mental health-related behaviour and learning, parent mental well-being, teacher well-being will be collected 6 and 18 months post-randomisation. Implementation factors will be measured throughout the study. Intention-to-treat analyses, accounting for clustering within schools and classes, will adopt a two-level random effects linear regression model to examine outcomes for the intervention versus control students. Unadjusted and analyses adjusted for baseline scores, baseline age, gender and family socioeconomic status will be conducted. ETHICS AND DISSEMINATION: Ethics approval has been received by the Human Research Ethics Committee at the University of Melbourne. Findings will be reported in peer-review publications, national and international conference presentations and research snapshots directly provided to participating schools and families. PRE-RESULTS TRIAL REGISTRATION NUMBER: Australian New Zealand Clinical Trials Registry (ACTRN12619000326190).