In this study we investigated whether source connectivity analysis of resting-state Magnetoencephalographic (MEG) activity could separate mild traumatic brain injury (mTBI) patients from age-and sex-matched controls. For each subject, we used artifact-free data recorded on three sessions to estimate intracranial sources which were then projected onto a standardized brain atlas for common reference. The statistical and topological properties of functional brain networks, estimated using Granger causality, were analyzed using MANOVA, with group and recording session as the independent variables and number of in-going and out-going connections in each atlas region as dependent variables. Overall, mTBI subjects showed a larger number of stronger connections compared to controls. The number and topology of in-going and out-going connections were significantly different across the two groups in areas involved with spatial memory, perception of visual space, emotion formation and processing, learning, and memory. Additionally, differences between patients and controls were decreasing across the three sessions indicating patient improvement. Our results suggest that connectivity analysis may be used as a reliable biomarker of mTBI and can also help with the diagnosis and assessment of patient recovery.