Cancer chemotherapy is frequently accompanied by adverse effects, such as diarrhoea and leukopenia, which lead to malnutrition and a decrease in the patients' quality of life. We previously demonstrated that an immune-modulating formula (IMF)-an enteral formula enriched with immunonutrients, whey-hydrolysed peptides, and fermented milk-had anti-inflammatory effects and protective effects on intestinal disorders in some experimental models. Here, we investigated whether nutritional treatment with the IMF could prevent 5-fluorouracil (5-FU)-induced adverse effects in rats. Rats were randomised into CTR and IMF groups, which received a control formula or the IMD supplemented formula ad libitum. Two weeks after starting the formula, rats were intraperitoneally injected with 5-FU (300 mg/kg) on day 0. The treatment with 5-FU decreased their body weights, food intake, and leukocyte counts, and worsened the diarrhoea score. However, the body weights, food intake, and leukocyte counts were significantly higher in the IMF rats than in the CTR rats on day 1. The IMF also delayed the incidence of diarrhoea and significantly preserved the villus heights in the jejunum on day 2. In conclusion, nutritional treatment with the IMF alleviated the adverse effects induced by 5-FU injection in rats.