Introduction and importance: We report a rare case of subacute recurrent in-stent thrombosis after vertebral artery stenting of the left intracranial segment. Case presentation: A 56-year-old man presented with V4 segment severe stenosis of the left vertebral artery. Stent (Apollo, 2.5 mm x 8 mm) implantation was performed for severe stenosis of the left vertebral artery. Approximately 48 h after operation, the patient developed dizziness and drowsiness. DSA showed stent thrombosis, which was treated by PTAS (Apollo, 2.5 mm x 13 mm), and the preoperative symptoms resolved. Two days later, symptoms of posterior circulation ischemia reappeared, DSA showed recurrence of stent thrombosis and CYP2C19 genotypic analysis showed intermediate metabolizers. Revision PTAS (Enterprise, 4.5 mm x 28 mm) was performed followed by administration of Ticagrelor instead of tirofiban. The patient showed good neurological outcomes. CTA performed both one week and four months after the operation showed that the blood flow of the left vertebral artery was unobstructed. Clinical discussion: Endovascular therapy is an alternative treatment for severe intracranial vascular stenosis, and reocclusion is one of the serious complications. Conclusion: our case report highlights that recurrent in-stent thrombosis maybe be caused by inadequate preoperative assessment and unsuitable therapeutic drug selection for the stents.