INTRODUCTION: Cluster randomised trials (CRTs) are studies in which groups (clusters) of participants rather than the individuals themselves are randomised to trial arms. CRTs are becoming increasingly relevant for evaluating interventions delivered in school settings for improving the health of children. Schools are a convenient setting for health interventions targeted at children and the CRT design respects the clustered structure in schools (ie, pupils within classrooms/teachers within schools). Some of the methodological challenges of CRTs, such as ethical considerations for enrolment of children into trials and how best to handle the analysis of data from participants (pupils) that change clusters (schools), may be more salient for the school setting. A better understanding of the characteristics and methodological considerations of school-based CRTs of health interventions would inform the design of future similar studies. To our knowledge, this is the only systematic review to focus specifically on the characteristics and methodological practices of CRTs delivered in schools to evaluate interventions for improving health outcomes in pupils in the UK. METHODS AND ANALYSIS: We will search for CRTs published from inception to 30 June 2020 inclusively indexed in MEDLINE (Ovid). We will identify relevant articles through title and abstract screening, and subsequent full-text screening for eligibility against predefined inclusion criteria. Disagreements will be resolved through discussion. Two independent reviewers will extract data for each study using a prepiloted data extraction form. Findings will be summarised using descriptive statistics and graphs. ETHICS AND DISSEMINATION: This methodological systematic review does not require ethical approval as only secondary data extracted from papers will be analysed and the data are not linked to individual participants. After completion of the systematic review, the data will be analysed, and the findings disseminated through peer-reviewed publications and scientific meetings. PROSPERO REGISTRATION NUMBER: CRD42020201792.