A 66-year-old man with thrombocytosis was brought to our hospital to undergo removal of a left ventricular thrombus. He had developed cerebral infarction 6 days before presenting to the hospital and suffered from right incomplete hemiparalysis. Blood tests on admission revealed his platelet count to be 124.3 × 104/μl. The urgent removal operation was performed under general anesthesia. For carrying out extracorporeal circulation (ECC), approximately three times as much heparin as expected was needed, as well as antithrombin III (AT III) administration. This met the definition of heparin resistance. The thrombus was removed and surgical left ventricular reconstruction was performed. Aspirin and warfarin were initiated on postoperative day 5. A bone marrow biopsy was performed on postoperative day 8, which revealed hypercellular marrow with megakaryocyte proliferation, and the patient was diagnosed as having essential thrombocythemia (ET). Although hydroxycarbamide administration started on postoperative day 10, his platelet count increased to 290.7 × 104/μl on postoperative day 13. The counts descended gradually, and on postoperative day 34, his platelet count reached the normal range and he was discharged from the hospital. In the perioperative period, his new neurologic abnormality did not appear. Addition of heparin, administration of AT III, and coating the cardiopulmonary bypass circuit with heparin or macromolecular polymer prevented clot formation and enabled safe ECC in a patient with ET and a high platelet count.