Various guidelines regarding surgical site infection (SSI) have recently been established. However, perioperative management of the wound and use of antibiotics have never been standardized completely in departments of neurosurgery in Japan. This survey investigated current perioperative management and administration of surgical antibiotic prophylaxis (SAP) and compared with guidelines intended to reduce SSI associated with neurosurgery in Japan. Questionnaires were distributed to members of the conference on Neurosurgical Techniques and Tools and the Japan Society of Aesthetic Neurosurgery via internet. The questionnaires asked about methods of perioperative management. A total of 255 members returned answers to the questionnaires. The questionnaires revealed that partial or no removal of the hair and hair shampooing at the day before surgery were performed in 96.1% and 88.1% of each institute following the World Health Organization (WHO) guidelines. Use of SAP at just before, during, and after surgery were 65.0%, 86.2%, and 63.0%, respectively. The postoperative period of use of intravenous SAP prolonged beyond 24 h in 80.0% against the recommendation of WHO. Perioperative management of wounds and use of SAP varies in institutes in Japan and some procedures were far different from the WHO guidelines. Japanese neurosurgeons should notice the prolonged SAP and comply with the WHO guidelines.