IntroductionChildhood overweight and obesity is prevalent in the first 5 years of life, and can result in significant health and economic consequences over the lifetime. The outcomes currently measured and reported in randomised controlled trials of early childhood obesity prevention interventions to reduce this burden of obesity are heterogeneous, and measured in a variety of ways. This variability limits the comparability of findings between studies, and contributes to research waste. This protocol presents the methodology for the development of two core outcome sets (COS) for obesity prevention interventions in children aged from 1 to 5 years from a singular development process: (1) a COS for interventions targeting physical activity and sedentary behaviour and (2) a COS for interventions targeting child feeding and dietary intake. Core outcomes related to physical activity and sedentary behaviour in children aged ≤1 year will also be identified to complement an existing COS for early feeding interventions, and provide a broader set of core outcomes in this age range. This will result in a suite of COS useful for measuring and reporting outcomes in early childhood obesity prevention studies, including multicomponent interventions.Methods and analysisDevelopment of the COS will follow international best practice guidelines. A scoping review of trial registries will identify commonly reported outcomes and associated measurement instruments. Key stakeholders involved in obesity prevention, including policy-makers/funders, parents, researchers, health practitioners and community and organisational stakeholders will participate in an e-Delphi study and consensus meeting regarding inclusion of outcomes in the COS. Finally, recommended outcome measure instruments will be identified through literature review and group consensus.Ethics and disseminationDeakin University Human Research Ethics Committee (HEAG-H 231_2020). The COS will be disseminated through peer-reviewed publications and engagement with key stakeholders.