Background: Although supraventricular tachycardia in complex congenital heart disease (CHD) has been reported after surgical repair, its exact electrophysiologic identification has been limited to intraatrial reentrant tachycardia (IART). Moreover, junctional tachycardia (JT) has not previously been described as a cause of late postoperative arrhythmia. Methods and Results: Since 1993, a total of 12 patients with complex congenital heart disease presented with atypical focal junctional tachycardia (JT). All medical records, standard electrocardiography and Holter monitoring were reviewed. An intracardiac electrophysiologic (EP) study was performed in 11 patients. Ten patients were in a post-Fontan palliation status (5.7% of total Fontan survivals). Late JT occurred more frequently in heterotaxy syndrome among the Fontan survivals (7/52 vs. 3/124; p<0.01). The commonest anatomy of the atrioventricular junction was complete AV canal in 8 patients. EP characteristics of atypical focal JT was as follows: (1) Various tachycardia mechanisms were identified (increased automaticity or a triggered mechanism in 6/11, and focal reentry in 5/11, including one concealed nodofascicular pathway ) (2) ventriculoatrial conduction during tachycardia was either dissociation (7/12) or variable (5/12) (3) All JTs were terminated by adenosine. Class III antiarrhythmic agent was effective in 5/6. His bundle ablation was performed in one Fontan patient, who already had pacemaker because of accompanying intractable IART and sinus node dysfunction. Conclusion: Paroxysmal focal JT may be a source of late term supraventricular tachycardia in patients with complex CHD. The suspected tachycardia mechanism was either automatic/triggered or reentrant. In all patients, JT was effectively terminated by adenosine injection.