Puncturing the atrial septum is frequently used in adults. In children, the transseptal puncture is less common, technically more demanding, and the rate of complications is not well described. We studied the feasibility and safety of this procedure in a retrospective analysis of 157 consecutive children undergoing transseptal puncture for radiofrequency catheter ablation of left atrial targets in two tertiary-care centres between 2005 and 2013. The median age of the patients at intervention was 12.5 years (1.1–18 years), with median weight of 42 kg (range 9.0–97.0 kg). Pre-excitation was found in 102 procedures, accessory pathway with exclusively retrograde conduction in 41, focal atrial tachycardia in nine, left-sided permanent junctional/reciprocating tachycardia-like accessory pathways in three, and atypical atrioventricular nodal re-entry tachycardia in two. All the procedures were guided by fluoroscopy. Additional imaging by transoesophageal echocardiography was used in three patients. Successful transseptal puncture was possible in 99.4% of the cases, ablation in 97.4%. The median time, including mapping and radiofrequency ablation, was 120 minutes (range 60–450), the median fluoroscopy time 10.8 minutes (range 1.8–75), and the median radiation dose 3 Gy cm2 (range 0.3–35). In total, five patients (3.2%) had a recurrent arrhythmia during the observation period of a median of 40 months (range 1–103). No complications associated with the transseptal puncture were observed. Transseptal puncture is a feasible and safe procedure in children. This access allows successful and efficient radiofrequency ablation of arrhythmia of the left atrium in the vast majority of the patients and might be considered as the first-line approach in this population.