The case was a 23-year-old male who presented with headache and fever. Because he was suspected to have a cerebral abscess from a brain CT examination performed by his former physician, the patient was admitted to our hospital. Neck stiffness was recognized and a cerebrospinal test confirmed an increased count of prevailing multinucleated cells. Although blood and cerebral-spinal cultures were found to be negative, we diagnosed his case as a brain abscess with a contrast-enhanced MRI examination. To explore the cause of the disease, we conducted a thorax, contrast-enhanced CT examination and found phymatoid lesions accompanied by inflow and outflow blood vessels at the right S6, which suggested the involvement of pulmonary arteriovenous malformation. Because a right-to-left shunt was found with transcranial Doppler sonography, we diagnosed a cerebral abscess caused by a pulmonary arteriovenous malformation. The cerebral abscess was improved by administering antibiotics, and we performed a segmentectomy of the lower lobe region under video-assisted thoracic surgery. Postoperative transcranial Doppler sonography did not show the right-to-left shunt, and the patient was discharged with no remaining neural-cataplectic symptoms.