Background Schools provide universal access to children over five years of age, representing a key opportunity for nutrition interventions to prevent the development of chronic disease. However, an important impediment to the large-scale adoption of evidence-based school nutrition interventions is the lack of evidence on effective strategies to implement them. This paper describes the protocol for a “Collaborative Network Trial” to support the simultaneous testing of different strategies undertaken by New South Wales Local Health Districts to facilitate the adoption of an effective school-based healthy lunchbox program (‘SWAP IT’). The primary objective of this study is to assess the effectiveness of different implementation strategies to increase school adoption of the SWAP across New South Wales Local Health Districts.Methods Within a Master Protocol framework, a collaborative network trial will be undertaken. Independent randomised controlled trials to test implementation strategies to increase school adoption of SWAP IT within primary schools in 10 different New South Wales Local Health Districts will occur. Schools within each Local Health District will be randomly allocated to either the intervention or control condition. Schools allocated to the intervention group will receive a combination of implementation strategies developed by each of the Local Health Districts independently, based on their existing capacities and local contexts. Across the 10 participating Local Health Districts, six broad strategies were developed and combinations of these strategies will be executed over a 6 month period. In six districts an active comparison group (containing one or more implementation strategies) was selected. The primary outcome of the trial will be adoption of SWAP IT, assessed via electronic registration records captured automatically following online school registration to the program. The primary trial outcome, between-group differences at 6 month follow-up, will be assessed using logistic regression analyses for each trial. Individual participant data component network meta-analysis, under a Bayesian framework, will be used to explore strategy-covariate interactions; to model additive main effects (separate effects for each component of an implementation strategy); two way interactions (synergistic/antagonistic effects of components), and full interactions.Discussion The study will provide rigorous evidence of the effects of a variety of implementation strategies, employed in different contexts, on the adoption of a school-based healthy lunchbox program at scale. Importantly, it will also provide evidence as to whether health service-centred, collaborative research models can rapidly generate new knowledge and yield health service improvements.