Abstract Background Balloon catheters are often used for pulmonary vein isolation (PVI) in atrial fibrillation (AF) because of their procedural efficiency. Apart from the established cryo-balloon (CB) catheter, there is a novel multi-electrode radiofrequency balloon catheter (RFB) with 3D mapping integration available. There is currently no data regarding a direct comparison of the RFB-PVI and the CB-PVI in a matched population. Objective Aim of this study was to assess the procedural data, the safety profile, and the outcome of the RFB-PVI and the CB-PVI. Methods This prospective registry study included patients with symptomatic paroxysmal or persistent AF, who underwent first-time PVI between January 2019 and April 2023, either with the RFB or the CB. For reduction of potential confounders patients were matched in a 1:2 ratio. Results In total 171 consecutive RFB patients and 342 matched CB patients were included. The baseline characteristics were comparable. The estimated recurrence free survival after 12 months was 81.3% in the RFB group and 76.8% in the CB group (p = 0.359). Longer procedural duration (p < 0.001) and longer fluoroscopy time was observed in the RFB group (p < 0.001). Except for the left inferior pulmonary vein, the single-shot isolation rate was comparable. In the RFB group no major complications occurred. In the CB group one transient ischemic attack, one pericardial tamponade, and two persistent phrenic nerve palsies occurred. Conclusion Although longer procedural duration was observed in the RFB group, both technologies enable an efficient and a safe PVI. Despite the 3D mapping integration of the RFB, no reduction in the fluoroscopy time was seen in comparison to the CB.