Background: The relationship between physical activity (PA) and academic achievement has received much attention given the recent push to increase children's PA levels through Comprehensive School Physical Activity Programs (CSPAP). Methods: In this study we followed 214 urban elementary students through an 8-month healthy school transformation that included both CSPAP and nutrition programming. Results: Program implementation was a significant predictor of students' reading comprehension rates of improvement, while students' aerobic fitness level, time two PA level, and level of program implementation were all significant contributors to students' rates of improvement in math. Conclusions: The importance of understanding healthy school transformations and their relationship with academic achievement in reading and math in urban elementary schools is discussed.