Abstract Background ‘Physical Activity 4 Everyone’ (PA4E1) was an efficacious multi-component school-based physical activity (PA) program targeting adolescents. PA4E1 has seven PA practices. It is essential to scale-up, evaluate effectiveness and assess implementation of such programs. Therefore, the aim is to assess the impact of implementation support on school practice uptake of the PA4E1 program at 12 and 24 months. Methods A cluster randomised controlled trial, utilising a type III hybrid implementation-effectiveness design, was conducted in 49 randomly selected disadvantaged Australian Government and Catholic secondary schools. A blinded statistician randomly allocated schools to a usual practice control (n = 25) or the PA4E1 program group (n = 24), with the latter receiving seven implementation support strategies to support school PA practice uptake of the seven practices retained from the efficacy trial. The primary outcome was the proportion of schools adopting at least four of the seven practices, assessed via telephone surveys with Head Physical Education Teachers and analysed using exact logistic regression modelling. This paper reports the 12-month outcomes. Results Schools were recruited from May to November 2017. At baseline, no schools implemented four of the seven practices. At 12 months significantly more schools in the program group had implemented four of the seven practices (16/24, 66.7%) than the control group (1/25, 4%) (OR = 33.0[4.15–1556.4], p < 0.001). The program group implemented on average 3.2 (2.5–3.9) more practices than the control group (p < 0.001, mean 3.9 (SD 1.5) vs 0.7 (1.0)). Fidelity and reach of the implementation support intervention were high (both > 80%). Conclusions Through the application of multiple implementation support strategies, secondary schools were able to overcome commonly known barriers to implement evidence based school PA practices. As such practices have been shown to result in an increase in adolescent PA and improvements in weight status, policy makers and practitioners responsible for advocating PA in schools should consider this implementation approach more broadly when working with schools. Follow-up is required to determine whether practice implementation is sustained. Trial registration Australian New Zealand Clinical Trials Registry ACTRN12617000681358 registered 12th May 2017.