Traumatic brain injury (TBI) is the leading cause of death and acquired disability in the pediatric population worldwide. We hypothesized that electroencephalography (EEG) synchrony and its temporal variability, analyzed during the acute phase following TBI, would be altered from that of normal children and as such would offer insights into TBI pathophysiology. Seventeen pediatric patients with mild to severe head injury admitted to a pediatric critical care unit were recruited along with 10 age- and gender-matched controls. Patients had two electroencephalographs performed 3 days apart. Outcome was measured at 1 year post-TBI utilizing the Pediatric Cerebral Performance Category score (PCPC). Maximal synchrony between EEG channels correlated to areas of primary injury as seen on computed tomography (CT) scan. The temporal variability of phase synchronization among EEG electrodes increased as patients recovered and emerged from coma (p < 0.001). This temporal variability correlated with outcome (Pearson coefficient of 0.74) better than the worst Glasgow Coma Scale score, length of coma, or extent of injury on CT scan. This represents a novel approach in the evaluation of TBI in children.