Mild traumatic brain injury (mTBI) may cause diffuse damage to the brain, especially to the frontal areas, that may lead to persistent symptoms. We studied participants with past mTBI by means of navigated transcranial magnetic stimulation (nTMS) combined with electroencephalography (EEG). Eleven symptomatic and 8 recovered participants with a history of single mTBI and 9 healthy controls participated. Average time from injury to testing was 5 years. The participants did not have abnormalities or signs of injury on brain magnetic resonance imaging, and they did not use any centrally acting medication. Left primary motor cortex (M1) and dorsolateral prefrontal cortex (DLPFC) were stimulated with nTMS and evoked potentials measured from the corresponding areas of both hemispheres. Delayed ipsilateral P30 and contralateral N45 peak latencies to left DLPFC nTMS were found in the symptomatic group, along with higher DLPFC N100 amplitudes compared with the control or recovered group. The recovered group had shorter P200 latencies in left DLPFC nTMS compared with the other groups. Both mTBI groups had higher motor thresholds compared with the control group. In left M1 nTMS, the mTBI groups showed less P30 amplitude increase, and the symptomatic group showed longer P60 interhemispheric latency difference with higher stimulation intensities. The results suggest altered brain reactivity and connectivity in mTBI. Some of the observed differences may be related to compensatory mechanisms of recovery. nTMS-EEG is a potentially useful tool for studying the effects of mTBI.