Background: Associations between school participation in an academic medical center-supported school-based wellness initiative and programmatic components implemented with change in average student body mass index (BMI) over time were examined. Methods: This was an observational study of 103 K-12 South Carolina schools over school years 2014-2018, classified as participating (n = 87 schools, 27,855 students) or non-participating (n = 16 schools; 3608 students). Associations between students' BMI z-score (BMIz) and school participation were evaluated by linear multilevel mixed-effects modeling using data from FitnessGram and the School Wellness Checklist© (SWC), respectively. Results: One-third of the students had a BMI percentile [greater than or equal to]85. Average student BMIz decreased in participating schools (p = 0.026) and increased in non-participating schools (p = 0.004) over time. For schools that participated two or more years, there was an inverse relationship between SWC score and student BMIz (p = 0.002) that did not differ by school type, rural/urban location, Title 1 status, or student sex. Physical activity and stress management interventions for students, as well as employee wellness and establishing a wellness committee at the school level were significantly associated with decreased average student BMIz (all p < 0.05). Conclusion: Implementation of similar comprehensive school-based wellness programs focused on improving physical activity, stress management, and employee engagement may help prevent and reduce pediatric obesity in diverse communities.