We investigated the effects of fermented rice bran (FRB) administration in two groups of C57BL/6J mice. The first group was fed with a high-fat diet, and the second group was fed with a high-fat diet supplemented with the FRB for 8 weeks. FRB supplementation suppressed the high-fat-induced weight gain and considerable alterations in the intestinal microbiota profile in the second group. Among 27 bacterial genera detected in the FRB, only Enterococcus, Lactobacillus, Bacteroides, Prevotella, and the unclassified family Peptostreptococcaceae were detected in mice feces. Their abundances were not particularly increased by FRB supplementation. The abundances of Enterococcus and the unclassified family Peptostreptococcaceae were even suppressed in the second group, suggesting that FRB supplementation didn’t cause an addition of beneficial microbiome but inhibit the proliferation of specific bacteria. Fecal succinic acid concentration was significantly decreased in the second group and highly correlated with the relative abundances of Turicibacter, Enterococcus, and the unclassified family Peptostreptococcaceae. A significant increase in fumaric acid and a decrease in xylitol, sorbitol, uracil, glutamic acid, and malic acid levels were observed in the peripheral blood of the second group. FRB supplementation counteracted the high-fat-induced obesity in mice by modulating the gut microbiota and the host metabolism.