The left ventricular assist device (LVAD) is a battery-operated, mechanical pump-type device that helps in maintaining the pumping ability of a failing heart. Thromboembolism poses a significant risk during and after LVAD implantation. It occurs in up to 35% of patients with adverse sequelae. We present the case of a 75-year-old man who underwent coronary artery bypass graft surgery and LVAD implantation for acute myocardial ischemia and severe left ventricular dysfunction. However, subsequent transthoracic echocardiographic examination revealed an LVAD thrombus, and LVAD removal was suggested following the failure of thrombolytic therapy. After the LVAD cannula was removed, transesophageal echocardiography (TEE) revealed a residual thrombus in the left atrium. Thrombectomy was successfully performed by opening the left atrium with cardiopulmonary bypass. We believe that TEE monitoring aided the implantation and removal of the LVAD device. In this case, we found that TEE not only helped in monitoring the ventricular function but also in detecting other problems such as the residual thrombus. We strongly recommend TEE monitoring during the entire LVAD-removal procedure, particularly for patients who need to undergo LVAD removal because of thrombosis formation.