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The present study examined gender differences in health, physical activity, physical fitness, real and perceived motor competence, and executive function indicators in three time points, and analyzed the dynamic and non-linear association between health, biological, behavioral, and cognitive variables in children followed over time. A total of 67 children (aged between six and 10 years) were followed during two years and split into two cohorts (six to eight years old: C1; eight to 10 years old: C2). Data regarding health, physical activity, real and perceived motor competence, physical fitness, and executive function indicators were obtained according to their respective protocols. Comparison tests and network analysis were estimated. Significant gender differences were found in both cohorts. The emerged networks indicated different topologies in both cohorts. No clusters were observed between the variables in C1, and there was a greater number of interactions at eight years of age. Sparse networks were observed in children aged eight and 10 years in C2, and greater connectivity was observed at nine years of age between health, physical fitness, motor competence, and physical activity indicators. This study showed that there are non-linear dynamic relationships between health, biological, behavioral, and cognitive variables over time during child development.