Left ventricular thrombus is life-threatening when it causes systemic embolization. In cases with a high risk of systemic embolization, left ventricular thrombectomy is recommended. However, the optimal surgical approach is unclear, especially for non-ischemic cardiomyopathy, because left ventriculotomy carries the risk of postoperative cardiac dysfunction. We herein report a male patient with multiple left ventricular thrombi due to acute myocarditis. Endoscopy-assisted left ventricular thrombectomy through right mini-thoracotomy was successfully performed. This method might be an efficient and less-invasive left ventricular thrombectomy for non-ischemic cardiomyopathy.