Essential thrombocythemia (ET) is a myeloproliferative disorder complicated by thrombosis in 13% of cases. The Janus kinase 2 (JAK2) V617F mutation is present in 60% of ET cases, and it has recently been reported that the mutation itself is a significant contributor to ischemic stroke. Here, we present an illustrative case of late in-stent thrombosis following carotid artery stenting (CAS) in a patient with ET and the JAK2 V617F mutation presenting with symptomatic internal carotid artery (ICA) stenosis. An 80-year-old man with a history of JAK2 V617F-positive ET suffered from left upper motor weakness and numbness. Magnetic resonance imaging/magnetic resonance angiography revealed multiple acute cerebral infarctions scattered in the right frontal and parietal lobes and right ICA stenosis. Despite continued antiplatelet therapy, plaque size did not decrease. CAS was performed one month later; however, five months after the procedure, instent thrombus growth was observed, leading to severe stenosis despite administering antiplatelet or anticoagulant drugs. The thrombus was eventually resolved with increased doses of hydroxyurea and aspirin administration. In conclusion, controlling platelets and inflammation with hydroxyurea and aspirin may help improve the condition in case of rapid thrombosis due to the JAK2 V617F mutation, unlike other thromboses. This case highlights the importance of careful follow-up after CAS.