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Objective: In-stent thrombosis (IST) is a known complication after stent-assisted coil (SAC) embolization. We report a case of mechanical thrombectomy using a stent retriever (SR) for IST and share our experience with this treatment to prevent a poor outcome in future cases. Case Presentation: The patient was a 62-year-old man. SAC embolization for an unruptured left internal carotid artery (ICA) aneurysm was performed. Three weeks after discharge, right hemiparesis and aphasia developed. Magnetic resonance imaging (MRI) demonstrated cerebral infarction in the left middle cerebral artery (MCA) territory and the left ICA was occluded. His relatives told us that the patient discontinued taking antiplatelet drugs. IST was diagnosed and emergency thrombectomy was performed. First, we tried to introduce an aspiration catheter or balloon catheter into the occluded lesion, but they were unable to be sufficiently inserted to the distal site. Therefore, we used a SR even though it carried a risk of friction on the deployed stent. The occluded artery was finally recanalized using the SR, but the stent became shortened. For the treatment strategy, sufficient medication (antithrombogenic agents and edaravone) should be administered first, followed by mechanical treatment. In mechanical treatment, thrombus fragmentation with a guidewire or balloon and aspiration should be attempted first. New aspiration catheters to carry the devices to the far distal site easily are now available. Conclusion: SRs cannot be utilized for thrombectomy with a stent. In emergency situations, careful consideration during troubleshooting rather than using a SR is needed.