A 26-year-old man presented with an unusual multilobulated cystic formation in the brain stem with normal pressure hydrocephalus, followed by fluctuating cyst volume and Benedikt's syndrome. Ventriculoperitoneal shunting to relieve the hydrocephalus caused an increased cystic size, resulting in worsened neurological deficits. Cystectomy and an additional shunt resolved the symptoms. Immunohistochemical and electron microscopic examinations of the surgical specimen revealed no epithelial lining but numerous astrocytic processes on the luminal surface, probably resulting from expansion of the cyst. This case suggests that cystectomy before shunt emplacement is recommended in similar cases.