The purpose of this study was to relate the factors of school-based physical activity and obesity with the academic achievement of a national longitudinal sample of students who entered school as Kindergarteners during the 1998-99 school year. Although several authors have focused on the health of children and how health issues may affect students in the school setting, there is little empirical research that specifically links school-based physical activity and obesity with academic achievement (American Association of School Administrators, 2006). The current study was based on the premise that the health of a child is multi-faceted and has an effect on his or her ability to learn and to achieve academically. Specifically, health-related topics of school-based physical activity and obesity were considered. The data were obtained from the United States Department of Education Longitudinal Study on the Kindergarten class of 1998-99 (Tourangeau, Nord, Lê, Pollack, & Atkins-Burnett, 2006). A multilevel growth model was conducted to explain the variation in Level 2 (campus-level) contextual predictors on Level 1 (student-level) means and slopes. M-plus (version 4.2) was employed to account for the clustered structure of the data where students were nested within schools. The results of the multilevel growth model indicated that academic achievement was particularly impacted by the demographic variable of student socioeconomic status. Initial baseline reading and math scores were positively impacted by campuses that provided students with more opportunities for physical activity, but this benefit did not persist over the time period being studied. Significant effects were found between body mass index (BMI) and growth of reading and math scores over the time period studied. Higher BMI scores were associated with lower reading and math scores, and this was evident over the time period studied.