The objective of this study was to characterize the functional activation of the neural correlates of voluntary regulation of emotion in soldiers both with and without chronic mild traumatic brain injury (mTBI). Using functional magnetic resonance imaging (fMRI) and a battery of cognitive and psychological health measures, we assessed differences between active-duty U.S. soldiers with chronic mTBI (n = 37) and without (Controls, n = 35). Participants were instructed to maintain (passively view), enhance, and suppress emotions associated with negative and neutral visual stimuli. The mTBI group showed significantly greater clinical symptoms, but only a mild decrement in attention. Group contrasts, while controlling for posttraumatic stress disorder (PTSD) symptoms, revealed a differential neural activation pattern compared to controls, but only during the enhance condition. Specifically, the mTBI group showed greater activation in the precentral gyrus, postcentral gyrus, inferior parietal lobe, insula, and superior temporal gyrus. Finally, the effect of PTSD symptoms during the enhance condition was associated with accentuated activation of the frontal and limbic regions implicated in both emotion regulation and PTSD. Hyperactivation of neural regions in the mTBI group during the enhance condition may reflect vigilance towards negative contextual stimuli and/or poor strategy that might result in suboptimal allocation of resources to regulate emotions.