Coagulation factor XIII (F13) deficiency has been known to be a rare disease with estimated one per two million and one of the possible reasons of postoperative hemorrhage; however, it still remains unpenetrated to physicians. We report a case of acute ventriculoperitoneal (VP) shunt dysfunction due to delayed intraventricular hemorrhage, which could be because of F13 deficiency. The patient was a 48-year-old man with a history of post-meningitis hydrocephalus followed by VP shunt placement. He was found unconscious and transferred to our hospital. A brain CT scan demonstrated shunt malfunction, and he underwent emergency shunt revision. The postoperative course was uneventful except for unexpected neck bruises and continuous minor bleeding from the surgical wound. Three days after surgery, he suddenly became comatose and a CT scan revealed the recurrence of hydrocephalus with newly identified small volume of intraventricular hemorrhage. Emergency shunt revision was performed again. The shunt valve was filled with a hematoma and bloody cerebrospinal fluid was drained from the ventricle. Postoperative blood sample examination demonstrated no abnormal findings but a decreased level of F13 activity, which was thought to be a possible cause of postoperative hemorrhage and the shunt valve hematoma. F13 deficiency causes delayed intracranial hemorrhage 24-48 h after neurological surgery. It can only be diagnosed by checking F13 activity with suspicion. If diagnosed accurately beforehand, unexpected postoperative bleeding can be preventable with proper treatment, such as F13 concentrate and cryoprecipitate. The actual number of the patient with F13 deficiency may be more than estimated ever.