A 57-year-old female presented with a left putaminal hemorrhage, intraventricular hematoma (IVH), and acute obstructive hydrocephalus. Neuroendoscopic surgery was performed for the IVH. Three days after successful IVH removal and improvement of her consciousness, the patient lapsed into a comatose state due to hydrocephalus caused by obstruction of the mesencephalic aqueduct by a small remnant clot. The small clot was identified by constructive interference with steady state magnetic resonance imaging and was removed during a second-look operation. Even after the cerebrospinal fluid circulation improves following neuroendoscopic surgery for IVH, the patient may nevertheless develop a life-threatening condition without warning signs in the subacute phase. Awareness of this complication will lead to early diagnosis and correct management.