Regular physical activity is beneficial to children’s physical, social and mental health. However, most children fail to meet the recommended 60+ min of moderate-intensity to vigorous-intensity physical activity every day. The Transform-Us! school-based and home-based intervention was developed to determine the impact of strategies to promote children’s moderate-to-vigorous physical activity versus reduce sedentary behaviour or a combination of these strategies, on behavioural and health outcomes. The main aim of this study was to determine the efficacy of the independent and combined intervention approaches to promoting physical activity and reducing sedentary behaviour on children’s moderate-to-vigorous physical activity and sedentary time after 18 and 30 months compared with usual practice. This study is a 30-month 2×2 factorial design cluster randomised controlled trial delivered in 20 primary schools with additional home intervention components. After recruitment, schools were then randomly allocated to one of four groups. Results show that Transform-Us! had stronger effects on children’s sedentary behaviour than physical activity in both the physical activity (PA) and sedentary behaviour (SB) interventions, and there were beneficial effects on children’s adiposity for both intervention approaches. However, no clear conclusions could be drawn regarding which intervention (PA or SB) had the strongest or more consistent effects on children’s health outcomes. Authors conclude that, based on their findings, government education departments and schools should consider adopting and implementing whole-of-school programmes to promote children’s physical activity and reduce sitting through active pedagogy and supportive social and physical environments at school and home to benefit children’s sedentary time and some markers of cardiometabolic health.