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This study was designed to find the best method to separate proanthocyanidins from other phenolic compounds extracted from pomegranate’s peel and to investigate their radical scavenging capacity. Water is used as an effective solvent for extracting antioxidant compounds from pomegranate’s peel (Punica granatum). The final extract contained closely related compounds not readily separable. Proanthocyanidins are the most potent antioxidant found in this extract and the purification and separation from other phenolic compounds is an important challenge. A comparison of two SPE cartridges, including silica-based C18 and aminopropyl for the isolation and purification of proanthocyanidins extracted from pomegranate’s peel, showed that the proposed SPE method with aminopropyl cartridge using alkalized aqueous acetone as eluent was more effective for the purification and the separation of extractable proanthocyanidins.