In this study, we investigated the effects of radish sprout ethanol extract (RSE) on inflammatory responses in the macrophages and a mouse model of colitis. RSE administration was found to effectively inhibit the phosphorylation of IκB and, in turn, the production of pro-inflammatory enzymes and cytokines in lipopolysaccharide-stimulated macrophages. In dextran sulfate sodium (DSS)-colitis mice, RSE administration prevented body weight and colon length reduction, while decreasing inflammation and mucosal necrosis. The diversity of the fecal microbiota was significantly increased in the group treated with RSE. In addition, RSE administration decreased the relative abundance of the phylum Proteobacteria, which includes many pathogens, and increased the abundance of the genus Akkermansia. Beta diversity analyses showed that RSE administration restored the gut microbiota composition close to that of healthy mice. For the first time, we identified glycosides of sinapic acid as part of hydroxycinnamic acids in RSE with colitis-alleviating effects. Notably, 1,2-O-disinapoyl glucoside substantially decreased nitric oxide generation in LPS-stimulated macrophages.