The purpose of this study is to test the efficacy of bioactive natural product berberine in the treatment of patients with atrial fibrillation (AF). Data of 45 paroxysmal AF patients treated with berberine and 43 age, gender, New York Heart Association functional classification score, and concomitant cardiovascular disease matched patients treated with amiodarone were analyzed retrospectively to examine conversion rate, average conversion time, average heart rate, and echocardiographic parameters. There was no statistical difference between berberine and amiodarone on conversion rate or echocardiographic parameters. Berberine treatment showed a significantly longer average time to conversion and higher heart rate during sinus rhythm (SR) than amiodarone. Echocardiographic parameters showed that E/A ratio and left atrial diameter were significantly improved after 6- and 12-month berberine treatment, but only E/A ratio improved significantly at the same time points after amiodarone treatment. This is the first report to specifically compare efficacy of berberine and amiodarone in the treatment of patients with AF. We find that berberine and amiodarone are equally effective for conversion of AF and maintenance of normal SR.