INTRODUCTION:Data supports that motor skills are an underlying mechanism that influence physical activity along with perceived motor and physical competence, but the relationship between motor skills and physical activity during the early years is unclear. The goal of this study, Promoting Activity and Trajectories of Health (PATH) for Children, is to examine and compare the immediate (pre-test to post-test) and sustained (3-year follow-up) effect of an intervention on motor performance, physical activity and perceived physical competence to a control condition (ie, standard practice) in preschool-age children. METHODS AND ANALYSIS:The PATH study is a two-cohort, randomised cluster clinical trial. 300 children between the ages of >3.5 to 5 years of age will be randomised to the motor skill intervention (n=153) or control (n=147) condition. Each assessment involves a measure of motor skill performance; product and process, seven consecutive days of physical activity monitoring and perceived physical competence. These measures will be assessed before and after the intervention (pre-test to post-test) and then each academic year across 3 years, grades kindergarten, first grade and second grade (3-year follow-up). To assess the clustered longitudinal effect of the intervention on outcome measures, random-effects models (eg, mixed model regression, growth curve modelling and structural equation modelling) will be used. The PATH study addresses gaps in paediatric exercise science research. Findings hold the potential to help shape public health and educational policies and interventions that support healthy development and active living during the early years. ETHICS AND DISSEMINATION:Ethical approval for this study was obtained through the Health Sciences and Behavioral Sciences Institutional Review Board, University of Michigan (HUM00133319). The PATH study is funded by the National Institutes of Health. Findings will be disseminated via print, online media, dissemination events and practitioner and/or research journals. TRIAL REGISTRATION NUMBER:NHLBI ClinicalTrials.gov Identifier, NCT03189862. Registered 17 August 2017, https://clinicaltrials.gov/ct2/show/NCT03189862.