The antioxidant activities of FSW and USW were determined by different standard methods. The results showed FSW extract compared to USW possessed more TPC and isoflavone aglycone contents, and had higher ABTS radical scavenging activity, ferric reducing antioxidant power, reducing power, hydroxyl radical scavenging activity and superoxide radical scavenging activity. Additionally, FSW extract exhibited greater protection against oxidative DNA damage induced by Fenton’s reagent. The results suggested that FSW with enhanced antioxidant capacity could provide a functional soy beverage to contribute to the health and nutritional status improvement of consumers.