Experience of catheter ablation of pediatric focal atrial tachycardia (FAT) is still limited. There are data which were gathered prior to the introduction of modern 3D mapping and navigation systems into the clinical routine. Accordingly, procedures were associated with significant fluoroscopy and low success rates. The aim of this study was to present clinical and electrophysiological details of catheter ablation of pediatric FAT using modern mapping systems. Since March 2003, 17 consecutive patients <20 years underwent electrophysiological study (EPS) for FAT using the NavX^® system (n = 7), the non-contact mapping system (n = 6) or the LocaLisa^® system (n = 4), respectively. Radiofrequency was the primary energy source; cryoablation was performed in selected patients with a focus close to the AV node. In 16 patients, a total number of 19 atrial foci (right-sided n = 13, left-sided n = 6) could be targeted. In the remaining patient, FAT was not present/inducible during EPS. On an intention-to-treat basis, acute success was achieved in 14/16 patients (87.5 %) with a median number of 11 (1–31) energy applications. Ablation was unsuccessful in two patients due to an epicardial location of a right atrial focus (n = 1) and a focus close to the His bundle (n = 1), respectively. Median procedure time was 210 (84–332) min, and median fluoroscopy time was 13.1 (4.5–22.5) min. In pediatric patients with FAT, 3D mapping and catheter ablation provided improved clinical quality of care. Catheter ablation may be considered early in the course of treatment of this tachyarrhythmia in symptomatic patients.