The antioxidative activities of Thai native soybeans [Glycine max (L.) Merr. SJ2] fermented with Aspergillus oryzae BCC 3088 were investigated. Compared to naturally-fermented soybeans, the methanol extract of soybeans fermented with A. oryzae BCC 3088 was more effective in antioxidative activity by scavenging ability on 1,1-diphenyl-2-picrylhydrozyl (DPPH) radicals, inhibitory activities against linoleic acid peroxidation, Fenton reaction-induced breakage of DNA, and protein oxidation. The results suggest that the enhanced antioxidative activity of soybeans fermented with A. oryzae BCC 3088 observed in various antioxidative model systems could be related to the increased total phenolic and flavonoid contents, a significant bioconversion of the isoflavone glucosides (daidzin + genistin) into their corresponding bioactive aglycones (daidzein + genistein), and the formation of 8-hydroxygenistein (8-OHG). Fermentation of soybeans with A. oryzae BCC 3088 results in higher levels of isoflavone aglycones, which may enhance health benefits over naturally fermented soybeans.