A 57-year-old woman with a wide-necked anterior communicating artery (Acom) aneurysm underwent stent-assisted coiling (SAC) due to aneurysm enlargement. Dual antiplatelet therapy was initiated 7 days before the operation, and systemic heparinization was performed while maintaining an activated clotting time (ACT) of approximately 300 s during the procedure. SAC was performed using a laser-cut closed-cell stent and bare platinum coils. At the end of the procedure, the Acom and right anterior cerebral artery (ACA) were occluded by in-stent thrombosis. Following local intra-arterial administration of 480000 U of urokinase, the Acom and right ACA were recanalized, accompanied by extravasation around the Acom aneurysm. A computed tomography (CT) scan revealed a right frontal hematoma, which did not enlarge after the administration of protamine sulfate. The hematoma disappeared spontaneously, and the patient recovered without any neurological deficits. Local administration of urokinase is an effective treatment for in-stent thrombosis. However, because the devices for SAC may cause mechanical injuries to the aneurysms, urokinase should be used cautiously for cerebral aneurysms, even if unruptured.