Purpose: Anticoagulation with heparin is required during catheter ablation of atrial fibrillation (AF) to reduce systemic thromboembolism. In this study, we aim to compare safety and efficacy outcomes between patients who receive protamine administration for reversal of heparin and those who do not, following cryoballoon-based pulmonary vein isolation (PVI) for AF. Methods: Patients with symptomatic paroxysmal or persistent AF despite ≥1 antiarrhythmic drug(s) were scheduled for PVI per the recent consensus recommendations. Some patients were administered protamine at the end of the procedure depending on the operator’s choice. Results: Among 380 patients [48.2 % male, 56 (20–86) years] that were enrolled, 188 patients received protamine at the end of the procedure. Baseline characteristics did not differ between groups (p > 0.05). Mean protamine dose was 39.1 ± 6.4 mg. Only 1 patient developed rash following protamine infusion. Hospital stay was significantly shorter in patients who were administered protamine (1 [1–5] vs. 2 [1–7] days, p < 0.001). Hematoma/pseudoaneurysm or femoral AV fistula requiring surgical or interventional repair in the femoral access site occurred in 2 (1.1 %) patients who received protamine and 12 (6.3 %) patients who did not (p = 0.011). Deep vein thrombosis was seen in 1 patient in whom protamine was not administered (p = 0.499). Conclusion: To the best of our knowledge, this is one of the largest series showing that protamine administration for heparin reversal in patients undergoing cryoballoon-based PVI allows quicker sheath removal and minimizes the risk of potential vascular complications without causing an increase in thrombotic events.