Water kefir (WK) is produced using WK grains containing beneficial bacteria and yeasts. It has antibacterial, anti‐inflammatory, anti‐diabetic, anti‐hyperlipidaemic, anti‐ulcerogenic, and antioxidant effects. The purpose of the research was to determine the effect of WK on irritable bowel syndrome (IBS). In this study, thirty‐two female Wistar‐Albino rats aged 3 months were randomly distributed to four groups: the control group (C), the WK group, the WK group with IBS (WK + IBS), and the IBS group. Results indicated that the IBS groups had higher white blood cell, lymphocyte, monocyte counts, and procalcitonin levels. The findings of WK + IBS group showed that WK improved against IBS. TNF‐α, NF‐kB expressions, and histopathological results significantly decreased after receiving WK treatment. In conclusion, ingestion of WK has prophylactic effects on IBS as exhibited through an in‐vivo murine model. The findings suggested that IBS may be prevented and treated with WK.