Introduction: Physical activity interventions have been a proven effective means of preventing or treating overweight and obesity in children and adolescents. The results of these interventions in many cases are based on the determination of the effect they produce on anthropometric evaluations, which allow the calculation of health indices. However, the effects of physical activity interventions on anthropometric assessments in Chilean children and adolescents have not been systematized. The objective of this study is to provide a detailed protocol for a systematic review with meta-analysis that synthesizes the available evidence on the effect of physical activity interventions on anthropometric indicators and health indices in Chilean children and adolescents and identifies the field-based methods and health indices most used for body composition stimation. Methods: This protocol was performed according to the PRISMA declaration. MEDLINE (PubMed), Web of Science, Scopus, and Scielo databases will be systematically searched. Eligible studies will include randomized controlled trials (RCTs), non-RCTs and pre-post studies. Conclusion: This systematic review and meta-analysis protocol is designed to provide up-to-date evidence that could significantly assist public health policy makers and implementers of physical activity interventions through evidence-based guidance and recommendations.