We report the first case of cerebral cyst infection by Helicobacter cinaedi, a fastidious spiral-shaped gram-negative rod bacterium. A 70-year-old man visited Tokyo Medical University Hospital with persisting fever since 2 weeks. He underwent surgery and radiotherapy for parapharyngeal space squamous cell carcinoma 10 years ago. The radiotherapy resulted in a cerebral cyst as a side effect, and an Ommaya reservoir was inserted into the cyst. Blood culture and analysis of the brain cyst fluid revealed the presence of spiral-shaped gram-negative rod bacteria, which were identified as H. cinaedi by polymerase chain reaction. Initially, we administered clarithromycin (400 mg per day). After H. cinaedi infection was confirmed, the treatment was changed to meropenem (MEPM 6 g per day). The patient was treated for 43 days in the hospital with intravenous meropenem, and his clinical course was satisfactory. On the 44th day, he was discharged and prescribed oral minocycline (MINO 200 mg per day). After discharge, the patient's H. cinaedi infection did not recur. Our case illustrated the wide clinical spectrum of H. cinaedi as well as the effectiveness of antibiotic therapy comprising MERM and MINO for treating central nervous system infection by this organism.