Despite the remarkable developments in neurosurgical and neuro-interventional procedures, the optimal treatment for large or giant partially thrombosed aneurysms with a mass effect remains controversial. The authors report a case of a partially thrombosed aneurysm with a mass effect, which was successfully treated by stent-assisted coil embolization. A 41-year-old man presented with headache. Brain computed tomography depicted an 18×18 mm sized thrombosed aneurysm in the interpeducular cistern. More than 80% of the aneurysm volume was filled with thrombus and the canalized portion beyond its neck measured 6.8×5.6 mm by diagnostic cerebral angiography. Stent-assisted endovascular coiling was performed on the canalized sac and the aneurysm was completely obliterated. Furthermore, most of the thrombosed aneurysm disappeared in the interpeduncular cistern was clearly visualized follow-up brain magnetic resonance imaging conducted at 21 months. The authors report a case of selective coiling of a large, partially thrombosed basilar tip aneurysm.