BACKGROUND Er-Miao-San (EMS) is used in traditional Chinese medicine. This study aimed to investigate the effect of different elution fractions of EMS on acute inflammation induced by carrageenan in the rat paw and the possible mechanisms of action. MATERIAL AND METHODS Different aqueous fractions of EMS added to an AB-8 macroporous resin column and eluted with 0, 30%, 60%, and 90% ethanol. The content of berberine was evaluated by ultra-performance liquid chromatography (UPLC). Following injection of carrageenan and elution fractions of EMS into the rat paw, the volume of edema, levels of prostaglandin E2 (PGE2), tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-1ß, and IL-10 in the rat tissue were quantified by enzyme-linked immunosorbent assay (ELISA). Myeloperoxidase (MPO) activity and nitric oxide (NO) levels were measured by spectrophotometry. RESULTS The 60% and 90% ethanol elution fractions of EMS contained berberine, and both inhibited edema after carrageenan injection, with inhibitory rates of 31.04-40.86% and 48.84-52.18%, respectively, and with a significant reduction in MPO activity and NO production. The 60% ethanol elution fraction of EMS significantly decreased IL-1ß levels and increased IL-10 levels, and the 30%, 60%, and 90% ethanol EMS elution fractions considerably reduced the levels of TNF-alpha. The 60% and 90% ethanol EMS elution fractions significantly reduced PGE2 levels in the rat paw. CONCLUSIONS The 60% and 90% ethanol elution fractions of EMS had an anti-inflammatory effect following injection of carrageenan in the rat paw.