This study aimed to characterize cognitive and neural mechanisms responsive to cognitive rehabilitation in patients with traumatic brain injury (TBI). We hypothesized that prefrontal cortex (PFC) would be modulated by training in the goal-based process of strategic learning. Thirteen patients are currently planned to undergo three functional magnetic resonance imaging (fMRI) scans with a seven-week cognitive training between the second and third scans. Patients showed no significant difference on brain activation between the first two scans but preliminary results showed significant increases in activations of the superior and middle frontal gyri, putamen, and cerebellum after the cognitive rehabilitation training. These results showed increased modulatory control over working memory, providing candidate neural mechanisms that may underlie cognitive improvements with cognitive training.