Limited evidence exists on the cost-effectiveness of interventions to prevent obesity and promote healthy body image in adolescents. The SHINE (Supporting Healthy Image, Nutrition and Exercise) study is a cluster randomised control trial (cRCT) aiming to deliver universal education about healthy nutrition and physical activity to adolescents, as well as targeted advice to young people with body image concerns who are at risk of developing disordered eating behaviours. This paper describes the methods for the economic evaluation of the SHINE cRCT, to determine whether the intervention is cost-effective as an obesity prevention measure. A public payer perspective will be adopted, with intervention costs collected prospectively. Within-trial cost-effectiveness analysis (CEA) and cost-utility analysis (CUA) will quantify the incremental costs and health gains of the intervention as compared with usual practice (ie, teacher-delivered curriculum). CEA will present results as cost per body mass index unit saved. CUA will present results as cost per quality-adjusted life year gained. A modelled CUA will extend the target population, time horizon and decision context to provide valuable information to policymakers on the potential for incremental cost offsets attributable to disease prevention arising from intervention. Intervention costs and effects will be extrapolated to the population of Australian adolescents in Grade 7 of secondary school (approximate age 13 years) and modelled over the cohort's lifetime. Modelled CUA results will be presented as health-adjusted life years saved and healthcare cost-savings of diseases averted. Incremental cost-effectiveness ratios will be calculated as the difference in costs between the intervention and comparator divided by the difference in benefit. Semi-structured interviews with key intervention stakeholders will explore the potential impact of scalability on cost-effectiveness. These data will be thematically analysed to inform sensitivity analysis of the base case economic evaluation, such that cost-effectiveness evidence is reflective of the potential for scalability. Ethics approval was obtained from the Deakin University Human Research Ethics Committee (#2017-269) and the Victorian Department of Education and Training (#2018_003630). Study findings will be disseminated through peer-reviewed academic papers and participating schools will receive annual reports over the 3 years of data collection. ACTRN 12618000330246; Pre-results.