Introduction: Self-regulation (SR) is critical to healthy development in children, and intervention approaches (i.e., professional training, classroom-based curricula, parent-focused intervention) have shown to support or enhance SR. However, to our knowledge, none have tested whether changes in children's SR across an intervention relate to changes in children's health behavior and outcomes. This study, the Promoting Activity and Trajectories of Health (PATH) for Children-SR Study uses a cluster-randomized control trial to examine the immediate effects of a mastery-climate motor skills intervention on SR. Secondly, this study examines the associations between changes in SR and changes in children's health behaviors (i.e., motor competence, physical activity, and perceived competence) and outcomes (i.e., body mass index and waist circumference) (ClinicalTrials.gov Identifier, NCT03189862)., Methods and Analysis: The PATH-SR study will be a cluster-randomized clinical trial. A total of 120 children between the ages of 3.5 to 5 years of age will be randomized to a mastery-climate motor skills intervention (n = 70) or control (n = 50) condition. SR will be assessed using measures that evaluate cognitive SR (cognitive flexibility and working memory), behavioral SR (behavioral inhibition), and emotional SR (emotional regulation). Health behaviors will be assessed with motor skills, physical activity, and perceived competence (motor and physical) and health outcomes will be waist circumference and body mass index. SR, health behaviors, and health outcomes will be assessed before and after the intervention (pre-test and post-test). Given the randomization design, 70 children in the intervention group and 50 in the control group, we have 80% power to detect an effect size of 0.52, at a Type I error level of 0.05. With the data collected, we will test the intervention effect on SR with a two-sample t-test comparing the intervention group and the control group. We will further evaluate the associations between changes in SR and changes in children's health behaviors and health outcomes, using mixed effect regression models, with a random effect to account for within-subject correlations. The PATH-SR study addresses gaps in pediatric exercise science and child development research. Findings hold the potential to help shape public health and educational policies and interventions that support healthy development 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-SR study is funded by the National Institutes of Health Common Fund. Findings will be disseminated via print, online media, dissemination events and practitioner and/or research journals., Trial Registration Number: ClinicalTrials.gov Identifier, NCT03189862., Competing Interests: National Institutes of Health (NIH): National Heart, Lung, and Blood Institute (NHLBI) R01-HL-132979. The funders had and will not have a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., (Copyright: © 2023 Robinson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)