IntroductionEfficacious programmes require implementation at scale to maximise their public health impact.TransformUsis an efficacious behavioural and environmental intervention for increasing primary (elementary) school children’s (5–12 years) physical activity and reducing their sedentary behaviour within school and home settings. This paper describes the study protocol of a 5-year effectiveness–implementation trial to assess the scalability and effectiveness of theTransformUsprogramme.Methods and analysisA type II hybrid implementation–effectiveness trial,TransformUsis being disseminated to all primary schools in the state of Victoria, Australia (n=1786). Data are being collected using mixed methods at the system (state government, partner organisations), organisation (school) and individual (teacher, parent and child) levels. Evaluation is based on programme Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework. RE-AIM domains are being measured using a quasi-experimental, pre/post, non-equivalent group design, at baseline, 12 and 24 months. Effectiveness will be determined in a subsample of 20 intervention schools (in Victoria) and 20 control schools (in New South Wales (NSW), Australia), at baseline, 12 and 24 months. Primary outcomes includeTransformUsReach, Adoption, Implementation and organisational Maintenance (implementation trial), and children’s physical activity and sedentary time assessed using accelerometers (effectiveness trial). Secondary outcomes include average sedentary time and moderate to vigorous-intensity physical activity on weekdays and during school hours, body mass index z-scores and waist circumference (effectiveness trial). Linear mixed-effects models will be fitted to compare outcomes between intervention and control participants accounting for clustering of children within schools, confounding and random effects.Ethics and disseminationThe trial was approved by the Deakin University Human Research Ethics Committee (HEAG-H 28_2017), Victorian Department of Education, the NSW Department of Education, Australian Catholic University (2017-145R), Melbourne Archdiocese Catholic Schools and Catholic Schools NSW. Partners, schools/teachers and parents will provide an informed signed consent form prior to participating. Parents will provide consent for their child to participate in the effectiveness trial. Findings will be disseminated via peer-reviewed publications, scientific conferences, summary reports to schools and our partner organisations, and will inform education policy and practice on effective and sustainable ways to promote physical activity and reduce sedentary behaviours population-wide.Trial registration numberAustralian Clinical Trials Registration Registry (ACTRN12617000204347).