Social networks influence children and adolescents' physical activity. The focus of this paper is to examine the differences in the effects of physical activity on friendship selection, with eye to the implications on physical activity interventions for young children. Prior to implementing a network intervention in the field, it is important to understand potential heterogeneities in the effects that activity level have on network structure. In this study, the associations between activity level and cross-sectional network structure, and activity level and change in network structure are assessed. We studied a real-world friendship network among 81 children (average age 7.96 years) who lived in low SES neighborhoods, attended public schools, and attended one of two structured aftercare programs, of which one has existed and the other was new. We modeled network selection effects and cross-sectional properties, while accounting for potential heterogeneities between networks. There was heterogeneity in the effect of physical activity on both cross-sectional network structure and the formation and dissolution processes, both across time and between networks. This suggests that if peer selection processes are changing within a network, a static network intervention strategy for childhood physical activity could become inefficient as the network evolves.