We previously showed that the water extracts of rice wine-baked Scutellaria baicalensis Georgi (RWBS) ameliorated colonic inflammation more than crude Scutellaria baicalensis (CS) after oral administration. The aim of this study is to compare the effect of rectal and oral administration of RWBS in the experimental colitis. Experimental colitis was induced in mice by daily treatment with 5% dextran sulfate sodium (DSS) in the drinking water for 7 days. Water was used as vehicle of oral administration, while Carbopol/PEG mucoadhesive gel was used as vehicle of rectal administration. RWBS and RWBS gel (RWBSG) were administered once per day for 7 days. RWBS and RWBSG significantly attenuated the disease activity index (DAI) calculated as the sum of scores of body weight loss, stool consistency and rectal bleeding. Furthermore, RWBS and RWBSG reduced the mucosal myeloperoxidase activity and COX-2 (cyclooxygenase-2) expression in colon tissue. Anti-inflammatory effect of CS on colonic inflammation was increased by baking with rice wine in both oral and rectal administration. Moreover, anti-inflammatory effects of oral administration on colonic inflammation was greater than those of rectal administration. Further study would be required for the development of intra-rectal formulation.