Diarrhea is a common adverse effect of antibiotics particularly that acts on anaerobes. Moutan Radicis Cortex (MRC) is an herbal medicine used for its anti-inflammatory and antibacterial actions. The purpose of this study was to analyze the active components of MRC to determine their effect on antibiotic-associated diarrhea (AAD) and anti-inflammatory effects. Of the various components of MRC, seven compounds (gallic acid, oxypaeoniflorin, paeoniflorin, ethyl gallate, benzoic acid, benzoylpaeoniflorin, paeonol) were identified and assessed for anti-inflammation effects. Paeonol was found to effectively reduce nitric oxide production and levels of IL-6 and TNF-α in a concentration-dependent manner. Paeonol also effectively reduced the mRNA expression level of IL-6, IL-1β, and TNF-α. Western blotting analysis confirmed the reduction of COX-2 and NF-κB levels; p-p38 MAPK levels increased in the presence of a low concentration (25 μM) of paeonol but decreased in the presence of a high concentration (50 μM). In the mouse model of lincomycin-induced AAD, all experimental groups treated with paeonol (25, 50, and 100 mg/kg concentrations) showed diminished diarrhea status scores. Finally, the expression levels of TNF-α and IL-4 were reduced compared with those in the control group. Therefore, paeonol may have active compounds of MRC to alleviate the diarrhea symptoms of AAD and reduce inflammatory mediators. Other components of the MRC extract could contribute to its known anti-inflammatory and antibacterial activity and should be tested for their possible activity.