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Abstract Background Persistent Atrial Fibrillation (PeAF) is a challenging case for rhythm control modalities. Catheter ablation is the mainstay in PeAF management; however, data regarding the comparative safety and efficacy of cryoballoon ablation (CBA) versus radiofrequency ablation (RFA) for PeAF is still limited. We aim to compare the safety and efficacy of CBA versus RFA for PeAF ablation. Methods We conducted a systematic review and meta-analysis synthesizing randomized controlled trials (RCTs), which were retrieved by systematically searching PubMed, EMBASE, Web of Science, SCOPUS, and Cochrane through October 2023. RevMan version 5.4 software was used to pool dichotomous data using risk ratio (RR) and continuous data using mean difference (MD) with a 95% confidence interval (CI). PROSPERO ID: CRD42023480314. Results Three RCTs with 400 patients were included. There was no significant difference between RFA and CBA regarding AF recurrence (RR: 0.77, 95% CI [0.50, 1.20], P = 0.25), atrial tachycardia or atrial flutter recurrence (RR: 0.54, 95% CI [0.11, 2.76], P = 0.46), and any arrhythmia recurrence (RR: 0.96, 95% CI [0.70, 1.31], P = 0.80). CBA was significantly associated with decreased total procedure duration (MD: − 45.34, 95% CI [− 62.68, − 28.00], P |