Background: School-environments are thought to be strong influences of behavioral choices. There is limited research available on the role of physical activity (PA) and school success among children with special health care needs (CSHCN). The purpose of this study was to explore differences in PA among CSHCN and non-CSHCN and how the school success index is related to PA in both groups. Methods: Data were taken from new version of the National Survey of Children's Health (NSCH), which consolidated questions from the previous NSCH and the National Survey of Children with Special Health Care Needs (NS-CSHCN). Chi-square and logistic regression analyses were employed to examine group differences. Results: There were significant differences among both subgroups, although most school-aged children did not meet recommended PA guidelines. Chi-squared analyses indicated; school engagement and the parent's perception of child safety at school were associated with the likelihood of meeting PA guidelines. Logistic regression analyses showed that the odds of meeting PA guidelines were associated with the school success index. Conclusions: Comprehensive school health programs should focus on PA both subgroups. School health educators should continue to advocate for safe and structured extracurricular activities to improve the child and adolescent's engagement and overall well-being.