Executive dysfunction is among the most common and disabling facets of cognitive impairment following traumatic brain injury (TBI), and may include deficits in reasoning, planning, mental flexibility, some aspects of attention and orientation, awareness and behavior. Rehabilitation programs based on cognitive-behavioral approaches to retrain planning and problem-solving and other executive deficits may improve such cognitive dysfunction. The purpose of this study is to investigate the effects of non-immersive virtual reality-based training to improve executive abilities and to reduce anxiety and depression symptoms in patients with TBI. Twenty patients with moderate to severe TBI were enrolled at our Neurorehabilitation Unit and divided to receive either the standard cognitive training or the virtual reality (VR) based cognitive training using the virtual reality rehabilitation system (VRRS-Evo). Each group received the same amount of rehabilitative training, including ROT (Reality Orientation Therapy) and Executive Training (ET), but using a different approach, i.e., a paper and pencil and an advanced approach. All patients were evaluated with a specific psychometric battery before (T0) and after the end (T1) of each program. Comparing pre- and post- treatment scores, in the VR-CT group, we found statistically significant differences in all administered outcome measures for cognitive and executive functioning, i.e., MoCA (p < 0.005), FAB (p < 0.005), TMT-A (p < 0.005), TMT-B (p < 0.005), TMT-BA (p < 0.001), and mood, i.e., HRS-D (p < 0.008). In the Conventional cognitive training (C-CT) group, we found a significant improvement only in MoCA (p < 0.03), FAB (p < 0.02) and in TMT-BA (p < 0.01). Coping strategies also improved, with better results in the VR-CT group. Our results suggest that VR rehabilitation, using the VRRS system, may be a valuable and motivational approach to improve visuo-executive abilities and coping strategies as well as mood in chronic TBI patients.