Doenjang (DJ), a fermented soybean product used in soups, stews, and sauces, contains high quality proteins, fats, vitamins, minerals, and other functional ingredients, including isoflavones and saponins. This study investigated whether DJ improves the bioavailability of isoflavones compared to boiled soybean (BS) in sham-operated or ovariectomized (OVX) rats. We also examined the effects of ovariectomy on the differences in bioavailability of isoflavones. BS and DJ were administered in sham-operated and OVX rats, and blood samples were collected. Twenty-six isoflavone-derived metabolites were identified. Pharmacokinetic analysis revealed that T values of the individual isoflavone metabolites were most different in sham and OVX rats, even after the same sample treatment; however, T values were significant different in a few metabolites such as daidzein 4'-glucuronide, daidzein 4'-sulfate, 2-(4-hydroxyphenyl)propionic acid, and benzoic acid. For most of the individual metabolites, C was higher in both sham and OVX rats administered BS than those administered DJ. The AUC was generally lower in OVX rats than in sham rats. The AUC of daidzein and genistein in BS-fed sham rats was approximately 1.7-fold higher than those administered DJ, whereas glycitein was detected only in the DJ group. No significant differences in AUC of daidzein and genistein were observed between BS and DJ administration in OVX rats, although the total isoflavone content of DJ was lower; thus, DJ-mediated isoflavone bioavailability was more effective in OVX rats. Similar tendencies were observed for phase II and gut-mediated metabolites. These results suggested that DJ enhanced isoflavone bioavailability under estrogen deficiency, even when the total isoflavone content was decreased by fermentation.