Abstract Background An atrioventricular node (AVN) ablation and permanent pacing have been previously reported as effective treatments for patients with atrial tachyarrhythmias. However single ventricle patients requiring chronic ventricular pacing are at a higher risk of developing ventricular dysfunction and atrioventricular valve regurgitation. We report a case of successful AVN ablation in a 3-month-old infant with hypoplastic left heart syndrome and ectopic atrial tachycardia (EAT). Case Summary A boy with hypoplastic left heart syndrome who had a refractory EAT resistant to various medications. At two months old, we performed an urgent radiofrequency catheter ablation of the EAT and the applications delivered at the cavo-atrial junction. Although it disappeared after the first catheter ablation for 2 weeks, it recurred on the next day after the diaphragm plication. At three months old and weighed 3.1 kg, we decided to perform an urgent AVN ablation of the EAT. The application was performed on the mid-septum of the tricuspid septum. A permanent pacemaker was implanted after the ablation. After the AVN ablation, the hemodynamics stabilized during the EAT. However, he died from a bacteremia infection at 4 months. Discussions This patient recieved an AVN ablation due to failure to previous radiofrequency catheter ablation and was hemodynamically stable with the dual chamber pacemaker. The AV block was successfully created by radiofrequency enegy on the mid-septum of the tricuspid annulus in this hypoplastic left heart syndrome patient. Pathological findings exhibited that the compact AVN was totally ablated without damage to the tricuspid leaflets or coronary artery.