Vinegars have been used as an alternative remedy for treating gout, but the scientific basis remains to be elucidated. In this study, seven commercial vinegars and one laboratory-prepared red-koji vinegar were evaluated for the inhibitory activity of xanthine oxidase (XO), a critical enzyme catalyzing uric acid formation. Red-koji vinegar exhibited potent xanthine oxidase inhibitory (XOI) activity and was used for isolating active compounds. The substances under two peaks with XOI activity from HPLC were identified as 5-hydroxymethyl-2-furfural (5-HMF) and 1-methyl-1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid (MTCA), by LC-MS-MS and NMR. The XO half-maximal inhibitory concentrations (IC(50)) of 5-HMF and MTCA were 168 and 860 μg/mL, respectively. In further mode-of-action analysis, the inhibitory mechanism of each compound was elucidated at the IC(50) level in the presence of various concentrations of xanthine as the substrate. The following Michaelis-Menten kinetics analysis of XO inhibition revealed uncompetitive and competitive patterns for 5-HMF and MTCA, respectively.