BackgroundPrevention of childhood obesity is a key approach to the primary prevention of noncommunicable diseases. Several models, based on the population health approach and aligned with ecological models, are used to design childhood obesity prevention programs around the world.ObjectiveThis study aims to introduce the design and evaluation plan of “Iran Healthy Start (IHS)/Aghazi Salem, Koodake Irani”—the customized Iranian version of Canadian Healthy Start/Départ Santé health promotion program—which is now being developed in Mashhad University of Medical Sciences (Mashhad, Iran) and focuses on improving physical activity and healthy eating among preschool children.MethodsWe will evaluate the intervention using a pilot randomized controlled design. The components of intervention include customized Decoda Web-based resources for children, an implementation guide for educators and managers, training and monitoring, communication and knowledge exchange, building partnership, and parent engagement. Outcomes include changes in anthropometry, physical activity level, nutritional risk status and dietary intake, and quality of life.ResultsThe project is funded by Mashhad University of Medical Sciences. The intervention was completed by the end of March 2018, and the analysis is currently under way. The first results of the IHS intervention program are expected to be submitted for publication in December 2018.ConclusionsThe double burden of malnutrition in early years children is a major health concern in developing countries. This justifies the need for health promotion programs that are specifically designed to target both overnutrition and undernutrition prevention. If the efficacy approved, the IHS could potentially be a comprehensive health promotion program for young children whose lifestyle behaviors can be improved toward a healthy future life in a nutrition transition setting.Trial RegistrationInternational Clinical Trials Registry Platform IRCT2016041927475N1; https://en.irct.ir/trial/22497International Registered Report Identifier (IRRID)RR1-10.2196/11329