Abstract Background Few large-scale, real-world studies have compared the safety of radiofrequency (RF) catheter ablations (CA) with that of cryoballoon ablations of atrial fibrillation (AF), especially in east Asian countries. Methods This retrospective, cross-sectional study used a nationwide administrative claims database, to compare complication-incidence rates between patients who underwent RFCA and cryoballoon ablation of AF. We used data from Medical Data Vision Co., Ltd, that is derived from the health claims, Diagnosis Procedure Combination (DPC) system, and flat-fee payment system in Japan. We first extracted hospitalization records with CA with diagnosis of AF. Exclusion criteria were 1) records with diagnoses of atrial flutter or atrial tachycardia, 2) patients aged <20 years old, 3) CA of AF performed other than RFCA or cryoballoon, 4) records with insufficient clinical data, and 5) patients who were prescribed both direct oral coagulants and warfarin. Complications were defined using the following ICD-10 diagnosis codes: major bleeding (I31.9, I97.1, J98.5, J048, J0021); thromboembolism (H342, I24, I269, I740, I741, I744, I748, I749, K550, K868, N280, or T790); ischemic stroke (G45, or I63); cardiac tamponade (I31.9, I97.1, or J98.5); and vascular access complications (hematoma: S701, S801, T140 or T810; and/or pseudoaneurysms: I72.4). Logistic regression analyses were performed to estimate odds ratios and 95% confidence intervals (CI) for major bleeding, systemic thromboembolism, ischemic stroke, and cardiac tamponade. Results Among the 32,797,540 records between June 2011 and August 2020 from 426 hospitals, 41,347 records who underwent CA of AF (Median 68 [60–74] years old, 30.2 % women) were included in the study. A total of 36,729 RFCA (88.8%) and 4,618 cryoballoon ablation (11.2%) cases were included in the cohort. Major bleeding, systemic thromboembolism, ischemic stroke, cardiac tamponade, and vascular access complications occurred in 194 (0.5%), 193 (0.5%), 116 (0.3%), 414 (1.0%) and 115 (0.3%) patients, respectively. As a result of logistic regression analysis, when cryoballoon ablation was used as a reference, RFCA was associated with higher risk of cardiac tamponade (OR 1.54, 95% CI 1.09–2.25, P = 0.02), while it was not associated with higher or lower risk of other complications (major bleeding OR [95% CI ]1.21 [0.77–2.04]; thromboembolism 1.74 [1.03–3.22]; ischemic stroke 1.88 [0.94–4.47]; vascular access complication; 1.00 [0.58–1.87]). Conclusion Compared to cryoballoon ablations, RFCA was associated with higher risk of cardiac tamponade, using nationwide administrative claims database.