The aim of the present study was to assess the feasibility, safety, and long-term results of remote magnetic navigation in arrhythmias associated with complex congenital heart disease (CHD). The improved outcomes for CHD resulted in an increased number of complex arrhythmias requiring distinctive ablation techniques. Thirty-six patients with CHD (age 35 ± 19 years, 21 male) were divided into 3 complexity groups and underwent 43 radiofrequency catheter ablation procedures using the magnetic navigation system (including 7 redo ablations) in combination with the CARTO RMT system. A total of 59 tachyarrhythmias were identified. Most patients had surgical scar-related tachycardia (25 focal, including 4 microreentrant atrial tachycardia, and 27 macroreentrant atrial tachycardia). Four accessory pathways and three ventricular tachycardias were diagnosed and treated. In 31 patients, ablation was successful, with an end point of noninducibility (86%). The success rate for CHD complexity of type I, II, and III was 50%, 88%, and 89%, respectively. The mean procedure and fluoroscopy time was 216 ± 101 minutes and 40 ± 34 minutes, respectively. The number of radiofrequency applications was 42 ± 47. No major complications related to the procedures occurred. Of the patients, 67% remained free of recurrence during a mean follow-up of 26 ± 4 months. Recurrence developed in 0%, 16%, and 45% of patients with CHD type I, II, and III, respectively. In conclusion, the magnetic navigation system is feasible to treat arrhythmias with reasonable success rates and good long-term outcomes in adult patients with CHD. The use of the magnetic navigation system offers advantages in complex anatomic situations.