IntroductionPhysical activity declines during adolescence, with the lowest levels of activity observed among those with disability. Schools are ideal settings to address this issue; however, few school-based interventions have been specifically designed for older adolescents with disability. Our aim is to investigate the effects of a school-based physical activity programme, involving high-intensity interval training (HIIT), on physical, mental and cognitive health in older adolescents with disability.Methods and analysisWe will evaluate the Burn 2 Learn adapted (B2La) intervention using a two-arm, parallel group, cluster randomised controlled trial with allocation occurring at the school level (treatment or waitlist control). Secondary schools will be recruited in two cohorts from New South Wales, Australia. We will aim to recruit 300 older adolescents (aged 15–19 years) with disability from 30 secondary schools (10 in cohort 1 and 20 in cohort 2). Schools allocated to the intervention group will deliver two HIIT sessions per week during scheduled specialist support classes. The sessions will include foundational aerobic and muscle strengthening exercises tailored to meet student needs. We will provide teachers with training, resources, and support to facilitate the delivery of the B2La programme. Study outcomes will be assessed at baseline, 6 months (primary endpoint), and 9 months. Our primary outcome is functional capacity assessed using the 6 min walk/push test. Secondary outcomes include physical activity, muscular fitness, body composition, cognitive function, quality of life, physical literacy, and on-task behaviour in the classroom. We will also conduct economic and process evaluations to determine cost-effectiveness, programme acceptability, implementation, adaptability, and sustainability in schools.Ethics and disseminationThis study has received approval from the University of Newcastle (H-2021–0262) and the New South Wales Department of Education (SERAP: 2021257) human research ethics committees. Findings will be published in peer-reviewed journals, and key stakeholders will be provided with a detailed report following the study.Trial registration numberAustralian New Zealand Clinical Trials Registry Number: ACTRN12621000884808.