A 77-year-old man presented with fever and back pain. Computed tomography revealed a distal arch aneurysm. Bacteroides fragilis was found in a blood culture, and we diagnosed a thoracic infected aneurysm. Because of the rapid enlargement of the aneurysm and his frailty, a TEVAR procedure was urgently performed. He left the hospital after antibiotic treatment with meropenem. However, he was re-hospitalized due to recurrence of the infection. The infection was well-controlled by treatment with intravenous meropenem, and the subsequent oral administration of metronidazole (MNZ). He was re-hospitalized again 7 weeks after discharge due to unsteady gait and articulatory disorder. MNZ-induced encephalopathy (MIE) was diagnosed because FLAIR brain magnetic resonance imaging revealed an area of high signal intensity in the bilateral basal dentate nuclei. These symptoms improved after MNZ was changed to AMPC/CVA. Fifteen months later, the patient was doing well and had no recurrence of the infection. We performed TEVAR for a patient with a thoracic aneurysm infected by B. fragilis. The recurrence of the infection was controlled by adequate antibiotic therapy, which included the administration of MNZ. However, patients who are treated with MNZ should be carefully observed to detect the development of neurological signs, as MNZ may induce encephalopathy. The early detection and withdrawal of metronidazole is important for the improvement of MIE.