A 72-year-old woman was scheduled to undergo aortic valve replacement for aortic stenosis when she was diagnosed with heparin-induced thrombocytopenia type II after a decrease in platelets was detected. Although postponement was considered, the operation went ahead as scheduled because of unstable hemodynamics. Continuous intravenous infusion of argatroban (4 mg/kg/min) was initiated at the start of the operation, and nafamostat mesylate (30 mg/h) was initiated when cardiopulmonary bypass was started. Activated coagulation time was monitored, and the dose of argatroban was adjusted accordingly. Argatroban administration was terminated after removal of aortic cross-clamping, and cardiopulmonary bypass was stopped 1 h later. The operation was completed 7 h after stopping cardiopulmonary bypass due to difficulties in hemostasis. Operation time was 12 h 21 min, cardiopulmonary bypass time was 3 h 10 min, blood loss was 3444 mL, and blood transfusion volume was 6400 mL. The amount of argatroban administered was lower in our case than in previously reported cases, but blood loss after stopping cardiopulmonary bypass could not be reduced in our case.