Purpose: Given the recent push to increase children's physical activity levels through whole-of-school approaches, the relationship between physical activity and academic achievement has received much attention. Therefore, this study sought to understand the relationship between academic achievement and healthy school transformations in urban elementary school children (4th grade; ~10 years old). Method: A total of 378 urban elementary students participated in an 8-month healthy school transformation that included both physical activity and nutrition programming. The Building Healthy Communities (BHC) program is a nutrition and physical activity program that has six main components: (1) principal engagement, (2) classroom physical activity and nutrition education, (3) active recess, (4) physical education, (5) healthy kids club, and (6) student leadership team. A path analysis was conducted to determine the relationship between the BHC healthy school transformation and student academic achievement. Results: The final model in the path analysis had a good model fit (x[superscript 2][subscript 20] = 28.43, p = 0.10; CFI = 0.991; TLI = 0.965; RMSEA = 0.03, 90% CI [-0.00-0.06]; SRMR = 0.03). In the final model, program fidelity was a significant predictor of students' reading comprehension rates of improvement, while students' aerobic fitness level and time two physical activity levels were all significant contributors to rates of improvement in math. Conclusions: Given recent suggestions to increase physical activity throughout the school day, understanding the relationship that comprehensive programming has on the academic achievement of children is needed. This study demonstrated a clear link between academic achievement and healthy school transformations and sets the stage for more research in this area, as well as implications for pedagogy around health and wellness in the school setting.