This report describes a 2-year-old male infant after repair of complicated congenital heart anomalies including common atrioventricular canal (CAVC), in which macroreentrant atrial flutter around the CAVC was demonstrated by electroanatomic mapping (CARTO) using a single catheter. Radiofrequency catheter ablation at the isthmus between the CAVC and the inferior vena cava eliminated the atrial flutter successfully.