A 6.5-year-old girl with short stature (height age, 3 years; bone age, 1.75 years) had isolated growth hormone deficiency. Preoperative computed tomography and magnetic resonance imaging demonstrated a large, well-demarcated, homogeneous mass above the dorsum sellae with a density consistent with flowing blood. Vertebral angiography showed a giant intracranial varix caused by an arteriovenous fistula that originated at the apex of the basilar artery. At operation, an aneurysm clip was placed at the origin of the fistula, and occlusion of the fistula was confirmed by intraoperative digital subtraction angiography. There were no permanent neurological sequelae. Despite shrinkage of the varix, demonstrated by follow-up computed tomography, growth hormone deficiency persisted postoperatively. Biosynthetic growth hormone therapy was initiated 6.5 months after surgery and resulted in a height increment of 8.2 cm after 9 months of treatment.