OBJECTIVE:: To quantify structural connectivity abnormalities in adolescents with mild traumatic brain injury (mTBI) and to investigate connectivity changes following aerobic training using graph theory and diffusion tensor imaging tractography. SETTING:: Outpatient research setting. PARTICIPANTS:: Twenty-two children (age: 15.83 ± 1.77 years, 10 females) with 4 to 16 weeks of persistent symptoms after mTBI and a matched healthy comparison group. DESIGN:: Randomized clinical trial of aerobic training and stretching comparison combined with case-control comparison. MAIN MEASURES:: (1) Five global network measures: global efficiency (Eglob), mean local efficiency, modularity, normalized clustering coefficient (γ), normalized characteristic path length (λ), and small-worldness (σ). (2) The self-reported Post-Concussion Symptom Inventory score. RESULTS:: At initial enrollment, adolescents with mTBI had significantly lower Eglob and higher γ, λ, and σ (all P < .05) than healthy peers. After the intervention, significantly increased Eglob and decreased λ (both P < .05) were found in the aerobic training group. Improvement in Post-Concussion Symptom Inventory scores was significantly correlated with the Eglob increase and λ decrease in the aerobic training and λ decrease in the stretching comparison group (all P < .05). CONCLUSION:: This pilot study showed initial evidence that structural connectivity analysis was sensitive to brain network abnormalities and may serve as an imaging biomarker in children with persistent symptoms after mTBI.