Objective: This study sought to examine the effects of the implementation of cognitive therapy program changes on patient outcomes in a post-acute care inpatient facility for brain injury rehabilitation. These changes include the implementation of a new cognitive therapy program, facilitated by licensed clinicians, that assesses and treats neurocognitive deficits in patients with brain injuries by using empirically supported techniques and individualized approaches in rehabilitation. Method: Data were collected on 548 residents at an inpatient post-acute care brain injury rehabilitation facility. The outcomes were evaluated using the Mayo-Portland Adaptability Inventory (MPAI) and the Level of Observation Tool (LOOT). The data were collected for two years prior to the implementation of the new program and for 2 years afterwards, between 2010–2013. The information was collected from persons with both traumatic and acquired brain injuries. Results: Measures of ability on the MPAI were significant (p < 0.05) and level of supervision required according to the LOOT approached significance (p = 0.053). These results were for the entire sample and TBI's, right and left CVA's, hypoxia/encephalopathy will be looked at separately. Conclusion(s): These findings show support for cognitive therapy in post-acute brain injury rehabilitation when treatment is facilitated by trained professionals who use empirically supported interventions and address deficits through individualized treatment planning approaches. The implementation of these changes has resulted in significant reduction in the level of care a patient requires post-treatment, as reflected by the improved patient outcomes in terms of their ability as reflected in the MPAI.