A 56-year-old man underwent cord blood transplantation for angioimmunoblastic T-cell lymphoma. He developed severe diarrhea and abdominal pain that persisted for more than 4 months. We suspected that he might have cord colitis syndrome (CCS), so metronidazole (MNZ) was administered. The patient's abdominal pain and diarrhea showed some improvement after the initiation of MNZ therapy, but they worsened on the cessation of MNZ, which prompted us to resume MNZ treatment. After the patient had taken MNZ (1500-2000 mg/day) for 78 days, he developed somnolence and dysarthria. We diagnosed him with metronidazole-induced encephalopathy (MIE) based on the characteristic magnetic resonance imaging findings and the clinical course. The patient's dysarthria and somnolence improved within a few days after the discontinuation of MNZ. CCS is a recently proposed clinical entity defined as a persistent diarrheal illness that is culture-negative, antibiotic-responsive, and not attributable to any known cause. Patients with CCS often have recurrent diarrhea after the discontinuation of MNZ and may require prolonged treatment for a median of 120 days. When treating CCS with MNZ, physicians should be alert for the development of MIE.