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Mild traumatic brain injury (mTBI) is a major public health concern. Functional MRI has reported alterations in several brain networks following mTBI. However, the connectome‐scale brain network changes are still unknown. In this study, sixteen mTBI patients were prospectively recruited from an emergency department and followed up at 4–6 weeks after injury. Twenty‐four healthy controls were also scanned twice with the same time interval. Three hundred fifty‐eight brain landmarks that preserve structural and functional correspondence of brain networks across individuals were used to investigate longitudinal brain connectivity. Network‐based statistic (NBS) analysis did not find significant difference in the group‐by‐time interaction and time effects. However, 258 functional pairs show group differences in which mTBI patients have higher functional connectivity. Meta‐analysis showed that “Action” and “Cognition …