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We report on changes in the ascending reticular activating system (ARAS) concurrent with the recovery of impaired consciousness following rehabilitation and cranioplasty in a patient with traumatic brain injury (TBI), which were demonstrated on diffusion tensor tractography (DTT). A 34-year-old male patient was diagnosed with a traumatic intracerebral hemorrhage after falling from a height of approximately 7 m and underwent a right frontoparietotemporal decompressive craniectomy and hematoma removal. At 5 months after onset, when starting rehabilitation, the patient showed impaired consciousness, with a Glasgow Coma Scale (GCS) score of 4. Comprehensive rehabilitative therapy was provided until 14 months after onset, and his GCS score improved to 8. Cranioplasty was performed using auto-bone at 14 months after onset. One month after cranioplasty, his GCS score improved to 12. On the 15-month DTT, the deviated lower dorsal ARAS was restored on both sides, and the right side had become thicker. The right lower ventral ARAS was reconstructed, and increased neural connectivity of the upper ARAS was detected in both the prefrontal cortices. Thus, changes in the ARAS were demonstrated in a patient with TBI during recovery of consciousness following rehabilitation and cranioplasty.