Left ventricular non-compaction (LVNC) is a congenital abnormality caused by arrest of the normal process of myocardial compaction, and the prognosis of LVNC is poor with progressing heart failure. Reports of cardiac operations in patients with LVNC are rare. We resected a right atrial myxoma in a 69-year-woman, who had suffered from severe heart failure and in whom echocardiogram indicated LVNC. Using myocardial protection for the immature myocardium, the postoperative course was uneventful and the patient was discharged 19 days after the operation. We must pay attention to cardiac function after discharge because of the poor prognosis.