This study examined the relationships between children’s reported levels of physical activity, body-mass index, self-esteem, and reading and mathematics scores, while controlling for sex, family structure, and socioeconomic status. The data were collected from the full population of Grade 6 students (N = 6,923) in New Brunswick (NB), Canada in 1996, as part of the Elementary School Climate Study, and the NB Department of Education’s Grade 6 Assessment. Physical activity had a negative relationship with body-mass index. Physical activity had a positive relationship with self-esteem, and a trivial negative relationship with academic achievement. The analysis revealed that both females and males who were more physically active had considerably higher levels of self-esteem. The study suggests that the relationship between physical activity and academic achievement is weak. For some children, physical activity may be indirectly related to enhanced academic performance by improving physical health and self-esteem.