ScopeThis study investigates the potential of glutamine to mitigate intestinal mucositis and dysbiosis caused by the chemotherapeutic agent 5‐fluorouracil (5‐FU).Methods and resultsOver twelve days, Institute of Cancer Research (ICR) mice are given low (0.5 mg kg−1) or high (2 mg kg−1) doses of L‐Glutamine daily, with 5‐FU (50 mg kg−1) administered between days six and nine. Mice receiving only 5‐FU exhibited weight loss, diarrhea, abnormal cell growth, and colonic inflammation, correlated with decreased mucin proteins, increased endotoxins, reduced fecal short‐chain fatty acids, and altered gut microbiota. Glutamine supplementation counteracted these effects by inhibiting the Toll‐like receptor 4/nuclear factor kappa B (TLR4/NF‐κB) pathway, modulating nuclear factor erythroid 2‐related factor 2/heme oxygenase 1 (Nrf2/HO‐1) oxidative stress proteins, and increasing mammalian target of rapamycin (mTOR) levels, thereby enhancing microbial diversity and protecting intestinal mucosa.ConclusionsThese findings underscore glutamine's potential in preventing 5‐FU‐induced mucositis by modulating gut microbiota and inflammation pathways.