Traumatic brain injury (TBI) is a chronic health condition. The prevalence of TBI, combined with limited advances in protocols to mitigate persistent TBI-related impairments in higher order cognition, present a significant challenge. In this randomised study (n = 60), we compared the benefits of Strategic Memory Advanced Reasoning Training (SMART, n = 31), a strategy-based programme shown to improve cognitive control, versus an active learning programme called Brain Health Workshop (BHW, n = 29) in individuals with TBI with persistent mild functional deficits. Outcomes were measured on cognitive, psychological health, functional, and imaging measures. Repeated measures analyses of immediate post-training and 3-month post-training demonstrated gains on the cognitive control domain of gist reasoning (ability to abstract big ideas/goals from complex information/tasks) in the SMART group as compared to BHW. Gains following the SMART programme were also evident on improved executive function, memory, and daily function as well as reduced symptoms associated with depression and stress. The SMART group showed an increase in bilateral precuneus cerebral blood flow (CBF). Improvements in gist reasoning in the SMART group were also associated with an increase in CBF in the left inferior frontal region, the left insula and the bilateral anterior cingulate cortex. These results add to prior findings that the SMART programme provides an efficient set of strategies that have the potential to improve cognitive control performance and associated executive functions and daily function, to enhance psychological health, and facilitate positive neural plasticity in adults with persistent mild impairment after TBI.