Ellagic acid is one of the most representative natural antioxidants, which is rich in pomegranate peel. In this study, a consecutive counter-current chromatographic (CCC) separation method was established to improve the preparative efficiency of ellagic acid from pomegranate peel. By optimizing solvent system, sample size, and flow rate, 280 mg of ellagic acid was obtained from 5 g of crude sample from pomegranate peel by CCC after six consecutive injections. Moreover, the EC 50 of ellagic acid in scavenging ABTS· + and DPPH· were 4.59 ± 0.07 μg/mL and 10.54 ± 0.07 μg/mL, respectively, indicating a strong antioxidant activity. This study not only established a high-throughput method for the preparation of ellagic acid, but also provided a successful example for the development and research of other natural antioxidants.