Basilar artery fenestration with multiple aneurysms is clinically rare, and treatment strategies remain controversial. This article reports a case of a patient admitted with dizziness and headache, digital subtraction angiography (DSA) revealed a basilar artery fenestration with unruptured “butterfly-wing” aneurysms. After discussion, stent-assisted coil embolization was performed, and postoperative angiography showed patency of the parent artery. On the second postoperative day, the patient developed lethargy, vomiting, and right-sided weakness, which was considered to be related to perioperative ischemia or inflammatory reaction. After adjusting antiplatelet therapy and adding low-dose corticosteroids, her symptoms improved. At discharge, she had right upper limb muscle strength grade 3, right lower limb grade 4, and mild dysarthria. At 2-month follow-up, she continued rehabilitation. This case suggests that the procedure is feasible, but the risk of perioperative complications is high, necessitating individualized decision-making and close monitoring.