Background: We report on a stroke patient with disorder of consciousness (DOC) who underwent repetitive transcranial magnetic stimulation (rTMS) and showed recovery of an injured upper ascending reticular activating system (ARAS) injury, which was demonstrated by using serial diffusion tensor tractography (DTT). Case presentation: A 45-year-old male patient was diagnosed as subarachnoid and intracerebral hemorrhages in the left fronto-parieto-temporal lobes. At 5 months after onset, the patient exhibited a persistent vegetative state, with a Coma Recovery Scale-Revised (CRS-R) score of 4. He underwent comprehensive rehabilitative therapy that included drugs for recovery of impaired consciousness and rTMS of the right dorsolateral prefrontal lobe. He recovered to a minimally conscious state (CRS-R: 13) at 7 months after onset and was transferred to a local rehabilitation hospital where he underwent similar rehabilitation but without rTMS. At 9 months after onset, his CRS-R score remained at 13. He was then readmitted to our hospital and underwent rehabilitation with rTMS until 10 months after onset. His CRS-R remained at 13, but his higher cognition had improved. The tract volume (TV) of the neural tract in the right prefrontal lobe in the upper ARAS on the 7-month DTT was higher than that on the 5month DTT. However, compared to the 7-month DTT, the right prefrontal lobe TV was lower on the 9-month DTT. On the 10-month DTT, the TV of that neural tract had again increased. Conclusions: Increases in neural TV in the right prefrontal lobe of the upper ARAS that were associated with the periods of rTMS application were demonstrated in a stroke patient with DOC.