Three-dimensional (3D) mapping and navigation systems have been widely used for the ablation of atrial fibrillation and ventricular tachycardia, but the applicability of these systems for the ablation of supraventricular tachycardia (SVT) due to right-sided accessory pathways (RAPs) remains unknown. The goal of this prospective randomized study was to compare the safety, efficiency, and efficacy of nonfluoroscopic and conventional fluoroscopic mapping techniques in guiding catheter ablation of SVT due to RAPs. Of the 393 consecutive patients with SVT who were randomized to receive either conventional fluoroscopic or Ensite NavX mapping-guided ablation, 64 patients with RAPs were included for analysis. Endpoints for ablation were no evidence of RAP conduction and no inducible atrioventricular reentrant tachycardia (AVRT). The 3D group showed fewer ablation pulses and a shorter total ablation time compared to the conventional group, although the acute procedural success did not differ significantly between the two groups. Total procedure time, electrophysiological study time, total fluoroscopy time, and cumulative radiation doses were also significantly reduced in the 3D group. Patients in the conventional group with a right atrium diameter (RAD) ≥ 47 mm required a longer fluoroscopy time. There was no significant difference in the recurrence rates between the two groups over a follow-up period of 3 to 29 months. There were no permanent complications. The 3D mapping system may be a preferred alternative for patients with AVRT due to RAPs, especially for patients with a large RAD (≥ 47 mm).