A fenestrated middle cerebral artery (MCA) is a rare congenital anomaly, and is related to interference in the normal embryonic development of the MCA. Fenestrated MCA has been regarded to have no clinical significance other than a rare event of hemorrhage from associated aneurysm. However, the fenestration within the arterial trunk can be an obstacle against thrombus migration and may be associated with a major cerebral infarction. Moreover, the presence of this anomaly can be hardly detected prior to thrombolytic procedures, and emergent treatments are proceeded without any information of anatomical configurations. Therefore, the recanalization procedures would carry a high risk of intraprocedural complications. We report a rare case of MCA territory infarction from occlusion of fenestrated M1 segment, and also introduce a safe method of mechanical thrombolysis using coil.