The mental health and wellbeing of young people has important consequences for students and society. Schools are a logical environment for management and early intervention of wellbeing, mental health and engagement with school. Interventions aimed at improving mental health and wellbeing in education systems requires knowledge of how wellbeing is clustered at a school level. Cluster-randomised trials, and regression analyses of such data also require knowledge of clustering. While school-level clustering in academic achievement has been well documented, less is known about school-level clustering of outcomes such as student wellbeing, school climate and school engagement, especially for students younger than 13 years. We calculated intraclass correlation coefficients (ICC) for 23 measures from the Wellbeing and Engagement Census (WEC) and five standardised tests of academic achievement from the Australian National Assessment Program, Literacy and Numeracy (NAPLAN) for 19,529 students from 376 government primary schools in South Australia. We compared these to ICC values for scores from standardised tests of numeracy and literacy. School supportiveness had the largest estimated ICC (0.08) among the WEC measures, meaning 8% of the total variance was attributed to differences between schools. All other WEC measures had ICCs of 0.05 or below, and academic scores had higher ICCs (0.11 to 0.16). Nearly all ICC estimates decreased after adjusting for either student- or school-level sociodemographic factors, with academic scores showing the largest relative decreases. These ICC values can be used for planning cluster-randomised trials, complex surveys or statistical analyses and to provide insights into the education system.