Cryoballoon (CB)-guided pulmonary vein isolation (PVI) represents a cornerstone in the treatment of atrial fibrillation (AF). Recently, a novel balloon-guided single shot device (POLARx, Boston Scientific) was designed. Our study aimed to compare the efficacy, safety and characteristics of the novel CB system with the established one (Arctic Front Advance (Pro), AFA, Medtronic). A total number of 596 patients undergoing CB-guided ablation for AF were included. 65 patients (65.0 ± 11.6, 31% female) undergoing PVI with the POLARx were compared to a cohort of 531 consecutive patients (63.0 ± 27.9, 25% female) treated with AFA. Acute PVI was achieved in all patients (n = 596, 100%). Total procedure duration (POLARx 113.3 ± 23.2 min, AFA 100.9 ± 21.3 min; p < 0.001) and fluoroscopy time (POLARx 10.5 ± 5.9 min, AFA 4.8 ± 3.6 min; p < 0.001) were significantly longer in the POLARx group. The POLARx balloon achieved significantly lower nadir temperatures (POLARx −57.7 ± 0.9 °C, AFA −45.1 ± 2.6 °C; p < 0.001) and a significantly higher percentage of pulmonary veins successfully isolated with the first freeze (p = 0.027 *). One major complication occurred in the POLARx (2%) and three (1%) in the AFA group. Both ablation systems are comparably safe and effective. AF ablation utilizing the POLARx system is associated with longer procedure and fluoroscopy times as well as lower nadir temperatures.