Acute bioprosthetic valve thrombosis can occur after surgery and sometimes cause hemodynamic instability and cardiogenic shock. Risk factors for bioprosthetic valve thrombosis are hypercoagulability, atrial fibrillation, atrial dilatation, low cardiac function, and lack of anticoagulation therapy. The authors present a case of severe mitral stenosis due to bioprosthetic valve thrombus. The patient was diagnosed with dilated-phase hypertrophic cardiomyopathy and underwent mitral valve replacement. He required venoarterial extracorporeal membrane oxygenation (VA-ECMO) due to extremely low cardiac output and was scheduled for left ventricular assist device (LVAD) implantation. Transesophageal echocardiographic examination before LVAD implantation revealed severe mitral stenosis due to bioprosthetic mitral valve thrombus, which was not detected by transthoracic echocardiography in the intensive care unit and contributed to the low cardiac function. The thrombus was removed through an unscheduled left atriotomy before LVAD implantation. The possibility of bioprosthetic valve thrombosis must be considered when the patient is dependent on VA-ECMO support. Early transesophageal echocardiographic examination of the bioprosthetic valve may be helpful and contribute to surgical decision-making.