Sufficient physical activity can help promote and maintain health, while its lack can jeopardize it. Since health and physical activity lay their foundation for later life in childhood and adolescence, it is important to examine this relationship from the beginning. Therefore, this scoping review aims to provide an overview of physical health indicators in children and adolescents in research on the effects of physical activity and sedentary behavior. We identified the indicators used to quantify or assess physical health and summarized the methods used to measure these indicators. We systematically searched Scopus, Pubmed, and Web of Science databases for systematic reviews. The search yielded 4595 records from which 32 records were included in the review. The measurements for physical health reported in the reviews contained measures of body composition, cardiometabolic biomarkers, physical fitness, harm/injury, or bone health. Body composition was the most used indicator to assess and evaluate physical health in children, whereas information on harm and injury was barely available. In future research longitudinal studies are mandatory to focus on the prospective relationships between physical activity or sedentary behavior, and physical health.