The purple yam, Dioscorea alata L., is an important source of starch, vitamins and polyphenols. Five different pigments from the purple tubers of this plant were separated by high-performance liquid chromatography-mass spectrometry, and the anthocyanin fraction (DACN) was collected. The anti-inflammatory effects of DACNs were investigated at different concentrations and compared with the standard colitis treatment, 5-aminosalicylic acid, in a trinitrobenzenesulfonic acid (TNBS)-induced colitis mouse model. Macro- and microscopic parameters including body weight change, disease activity index (DAI) and intestinal histology were used for the determination of the anti-inflammatory effects of DACNs. The gene expression levels of tight junction-related proteins in the intestine, myeloperoxidase activity, inducible nitric oxide synthase activity in colonic tissues and pro-inflammatory cytokine production in serum were also measured to elucidate the mechanism of DACN action. Eighty micrograms of DACNs per kilogram of body weight produced potent anti-inflammatory effects in the mouse model of inflammatory bowel disease (IBD), as shown by the DAI (2.78 ± 0.38 vs. 0.44 ± 0.51). Therefore, DACNs may be applied as a potential food supplement in IBD therapy.