Individual neurological complication caused by Herpes simplex viruses in neonates is well-known. We report neonatal Herpes encephalitis that caused multiple neurological complications in the same patient during acute phase of illness. Our patient differs from previously reported cases in the following ways: 1) Late onset neonatal presentation; 2) Development of multiple neurologic complications during acyclovir therapy; 3) Cesarean-section did not prevent perinatal transmission of Herpes simplex virus; and 4) Our patient’s acute hydrocephalus was managed conservatively and he had no reoccurrence of seizure, hydrocephalus, and no motor deficits. A high degree of suspicion, timely needed supportive medical and surgical care, and prompt initiation of intravenous acyclovir offer the best chance for neurological outcome in neonates with Herpes encephalitis.