Transcatheter ablation is an effective method to eliminate the arrhythmogenic substrate in symptomatic children with various types of arrhythmias. A reduction in the procedure and fluoroscopy time would decrease the hazardous effects of the ablation procedures. The magnetic navigation system (MNS) uses atraumatic catheters and facilitates accurate catheter placement in all regions of the heart for mapping and therapy delivery. We compared the efficacy and safety between a manual and MNS-guided approach for mapping and ablation of arrhythmias in a general pediatric arrhythmia population and in a subgroup of young children aged <10 years old. A total of 58 pediatric patients (mean age 12.2 ± 3.2 years) were included in the present study. Of the 58 consecutive patients, 29 were treated with the MNS and 29 underwent conventional manual ablation. No demographic differences were present between the 2 groups. Acute success was achieved in 26 of 29 patients and 27 of 29 patients (p = NS). The mean procedure and fluoroscopy times were comparable in both study groups (168 ± 56 minutes vs 183 ± 52 minutes, p = NS; and 22 ± 59 minutes vs 30 ± 29 minutes, p = NS). In young children (aged <10 years), the success rate did not differ between the 2 groups (10 of 11 vs 6 of 8, p = NS). However, significant decreases in the procedure and fluoroscopy times were achieved (139 ± 57 minutes vs 204 ± 49 minutes and 13 ± 7 minutes vs 31 ± 28 minutes, respectively; p = 0.01 and p = 0.04). In conclusion, our data have strongly suggested that using the MNS for treating young children is advantageous, because it significantly reduced the procedure and fluoroscopy times without compromising efficacy.