The purpose of this study was to evaluate the impact of an existing physical fitness program (CHAMPIONS) implemented during physical education on health-related indices (BMI percentile, waist circumference, cardiorespiratory endurance), self-perceptions, academic performance, and behavioral conduct over a school year. Students in three intervention (n = 331) and three control (n = 745) middle schools participated in the study that included assessments at pre-, mid-, and post-intervention. Multivariate repeated measures analyses indicated that boys and girls in CHAMPIONS compared favorably (p < .0125) to Controls at post-intervention on cardiorespiratory endurance, and boys significantly improved on BMI percentile from pre- to mid- and post-intervention (p < .0125). Students in CHAMPIONS maintained healthy BMI percentile and waist circumference values over the year. Findings provide preliminary evidence that CHAMPIONS is effective in improving or maintaining physical health indices among middle school youth.