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Individual differences in brain network modularity at baseline can predict improvements in cognitive performance after cognitive and physical interventions. This study is the first to explore whether brain network modularity predicts changes in cortical brain structure in 8‐ to 9‐year‐old children involved in an after‐school physical activity intervention (N = 62), relative to children randomized to a wait‐list control group (N = 53). For children involved in the physical activity intervention, brain network modularity at baseline predicted greater decreases in cortical thickness in the anterior frontal cortex and parahippocampus. Further, for children involved in the physical activity intervention, greater decrease in cortical thickness was associated with improvements in cognitive efficiency. The relationships among baseline modularity, changes in cortical thickness, and changes in cognitive performance were not present in the wait‐list control group. Our exploratory study has promising implications for the understanding of brain network modularity as a biomarker of intervention‐related improvements with physical activity. The present study is the first to show that brain network modularity at baseline predicted change in brain structure in children involved in a physical activity intervention. Further, intervention‐related changes in cortical thickness were associated with changes in cognition. The associations between modularity, change in cortical thickness, and cognition were not present in a wait‐list control group. The results have implications for modularity as a biomarker of intervention‐related changes with physical activity. [ABSTRACT FROM AUTHOR]