A 46-year-old man was admitted to our hospital for near syncope and palpitations. An electrocardiogram showed a common type of atrial flutter (AFL) with 1:1 atrioventricular conduction. Transthoracic echocardiography revealed a massive right atrial (RA) thrombus with a huge RA and right ventricle. The patient was diagnosed with arrhythmogenic right ventricular cardiomyopathy. It was difficult to control the heart rate with beta-blockers during AFL, which resulted in the deterioration of right-sided heart failure. The effect of anticoagulation therapy for the RA thrombus was also limited. Restoration to sinus rhythm by catheter ablation effectively improved the right-sided heart failure, and the massive RA thrombus eventually disappeared.