Previous studies have shown inconsistent results in clinical effectiveness between cryoballoon ablation (CBA) and radiofrequency ablation (RFA), and cost assessment between the procedures is important. The aim of this study was to evaluate the clinical effectiveness and cost-effectiveness between the procedures in patients with paroxysmal atrial fibrillation (AF) refractory to antiarrhythmic drug therapy. A systematic review and meta-analysis were performed. The primary outcome for the meta-analysis was long-term AF recurrence. Following the results of the meta-analysis, the cost-effectiveness of CBA versus RFA in Japan was assessed. The meta-analysis included 12 randomized controlled trials and six propensity-score matching cohort studies. AF recurrence was slightly lower in patients referred for CBA than for RFA, with an integrated risk ratio of 0.93 (95% confidence interval: 0.81-1.07) and an integrated hazard ratio of 0.96 (95% confidence interval: 0.77-1.19), but no significant difference was found. A cost-minimization analysis was conducted to compare the medical costs of CBA versus RFA because there was no significant difference in the risk of AF recurrence between the procedures. The estimated costs for CBA and RFA were JPY 4 858 544 (USD 32 390) and JPY 4 505 255 (USD 30 035), respectively, with cost savings for RFA of JPY 353 289 (USD 2355). Our meta-analysis suggests that CBA provides comparable benefits with regard to AF recurrence compared with RFA, as shown in previous studies. Although the choice of treatment should be based on patient and treatment characteristics, RFA was shown that it might be cost saving as compared to CBA.