This study evaluated the ameliorative effects of Korean-red-ginseng-derived polysaccharide (KRG-P) on antibiotic-associated diarrhea (AAD) induced by administering lincomycin in mice. Changes of intestinal barrier proteins, the intestinal microbiome and short-chain fatty acid (SCFA) contents were investigated. Lincomycin was orally administered for 9 days to induce diarrhea; subsequently, 100 mg/kg and 300 mg/kg of KRG-P were administered orally for 12 days. The diarrhea was observed in the AAD group; further KRG-P administration improved the diarrhea. Analysis of changes in the intestinal microbial flora of the mice revealed that the harmful bacterial flora (such as Proteobacteria) were increased in the AAD group, whereas beneficial bacterial flora (such as Firmicutes) were decreased. However, KRG-P administration resulted in decreased Proteobacteria and increased Firmicutes, supporting the improvement of the microbial flora imbalance caused by AAD. Moreover, an analysis of the SCFAs (acetic acid, propionic acid, and butylic acid) in the caecum revealed that SCFAs' contents in the AAD group were substantially reduced but tended to increase upon KRG-P administration. Based on these results, KRG-P, which is primarily composed of carbohydrates can improve lincomycin-induced diarrhea, likely owing to the recovery of SCFA content by improving the intestinal microbial imbalance and intestinal barrier proteins.