Background: 5-Fluorouracil (5-FU) is a common chemotherapeutic medication used to treat cancer. However, the intestinal tract may sustain oxidative damage as a result. Objectives: The purpose of this study was to clarify the underlying molecular mechanisms and examine the preventive benefits of cereal-based fermented drinks (CFBs) against intestinal injury in mice caused by 5-FU. Methods: The mice were injected intraperitoneally with 5-FU to induce intestinal mucosal and treated with CFB. The factors for intestinal barrier integrity, oxidative stress and inflammation were measured. Results: The findings demonstrated that CFBs had high levels of polyphenol, flavonoids, and peptides and had in vitro high free radical scavenging capacity. Furthermore, CFBs effectively ameliorated 5-FU-induced intestinal epithelium damage, characterized by increasing intestinal tight junctions and reducing apoptosis in intestinal cells. These protective effects may attribute to the increased activity of antioxidant-related enzymes (SOD, CAT, and GSH) as well as decreased amounts of inflammatory and oxidative damage markers (IL-1β, TNF-α, and MDA) in the intestinal tract. Conclusions: Overall, these results show that CFBs can mitigate intestinal damage caused by 5-FU by reducing oxidative stress, suggesting the potential utility of CFBs for therapeutic treatment against intestinal mucositis.