Introduction: Radiofrequency catheter ablation (RFCA) is widely used to treat atrial fibrillation (AF) in China. Objective: We aimed to determine the long-term cost effectiveness of RFCA versus antiarrhythmic drugs (AADs) in treating AF from the perspective of third-party payers. Methods: The model was structured as a 12-month decision tree leading to a Markov model that simulated the follow-up treatment outcomes and costs with time horizons of 8, 15, and 20 years. Comparators were standard-of-care AADs. Clinical parameters captured normal sinus rhythm, AF, stroke, post-stroke, intracranial hemorrhage (ICH), gastrointestinal bleeding, post-ICH, and death. The risk of operative death, procedural complications, and adverse drug toxicity were also considered. The model output was quality-adjusted life-years (QALYs) and incremental cost per QALY gained. Results: RFCA incurred more costs than the AADs but resulted in more QALYs gained than did AADs. The incremental cost per QALY gained with RFCA versus AADs was ¥66,764, ¥36,280, and ¥29,359 at 8, 15, and 20 years, respectively. The sensitivity analyses showed that the results were most sensitive to the changes in RFCA cost and CHADS 2 score (clinical prediction rule for assessing the risk of stroke in patients with non-rheumatic AF). Conclusion: Compared with AADs, RFCA significantly improves clinical outcomes and QALYs among patients with paroxysmal or persistent AF. From the Chinese payer’s perspective, RFCA is a cost-effective therapy over long-term horizons. © 2019, Springer Nature Switzerland AG.