Toki-shakuyaku-san (TOKI) is a Japanese kampo medicine, which consists of a mixture of herbal medicines and considered to be a promising remedial agent due to its immunomodulatory and anti-inflammatory effects. We examined the beneficial effects of TOKI in inflammatory bowel disease associated with the inflammation of the intestinal barrier. A study was designed, using C57BL/6 female mice and were administered with 3% DSS in drinking water for 8 days with or without 1 g/kg/day TOKI orally for the last 3 days and a normal group supplied with plain drinking water for 8 days. TOKI treatment attenuated the clinical symptoms of acute murine colitis and also alleviated the inflammatory mechanism by reducing the inflammatory mediators, such as IL-1β, IL-2, TGF-β, RAGE and TLR2. It has also decreased the levels of CHOP, caspase12, cleaved caspase3 and cleaved caspase7 and thereby down-regulated the endoplasmic reticulum stress and apoptotic signaling induced by DSS. Moreover, the expression levels of cyclin D1 and c-kit have also confirmed the beneficial role of TOKI in colitis. All these data suggested that TOKI can be a promising agent for the treatment of colitis since it alleviates the disease progression and severity.