Abstract: Background: Cluster randomised trials (CRTs) are increasingly used to evaluate non-pharmacological interventions for improving child health. Although methodological challenges of CRTs are well documented, the characteristics of school-based CRTs with pupil health outcomes have not been systematically described. Our objective was to describe methodological characteristics of these studies in the United Kingdom (UK). Methods: MEDLINE was systematically searched from inception to 30th June 2020. Included studies used the CRT design in schools and measured primary outcomes on pupils. Study characteristics were described using descriptive statistics. Results: Of 3138 articles identified, 64 were included. CRTs with pupil health outcomes have been increasingly used in the UK school setting since the earliest included paper was published in 1993; 37 (58%) studies were published after 2010. Of the 44 studies that reported information, 93% included state-funded schools. Thirty six (56%) were exclusively in primary schools and 24 (38%) exclusively in secondary schools. Schools were randomised in 56 studies, classrooms in 6 studies, and year groups in 2 studies. Eighty percent of studies used restricted randomisation to balance cluster-level characteristics between trial arms, but few provided justification for their choice of balancing factors. Interventions covered 11 different health areas; 53 (83%) included components that were necessarily administered to entire clusters. The median (interquartile range) number of clusters and pupils recruited was 31.5 (21 to 50) and 1308 (604 to 3201), respectively. In half the studies, at least one cluster dropped out. Only 26 (41%) studies reported the intra-cluster correlation coefficient (ICC) of the primary outcome from the analysis; this was often markedly different to the assumed ICC in the sample size calculation. The median (range) ICC for school clusters was 0.028 (0.0005 to 0.21). Conclusions: The increasing pool of school-based CRTs examining pupil health outcomes provides methodological knowledge and highlights design challenges. Data from these studies should be used to identify the best school-level characteristics for balancing the randomisation. Better information on the ICC of pupil health outcomes is required to aid the planning of future CRTs. Improved reporting of the recruitment process will help to identify barriers to obtaining representative samples of schools.