Intestinal mucositis is a common complication associated with 5‐Fluorouracil (5‐FU) treatment, a chemotherapeutic agent widely used for cancer treatment. Characterized by inflammatory and/or ulcerative processes, intestinal mucositis is pathophysiologically based on the promotion of direct damage to the epithelium resulting from oxidative stress from the generation of reactive oxygen species (ROS). Flavonoids such as rutin, troxerutin and isoquercitrin, obtained from D. Gardnerian, have been reported with antioxidant and anti‐inflammatory properties. The present study aimed to evaluate the effect of flavonoids obtained from D. Gardnerian on 5‐fluorouracil‐induced intestinal mucositis in Swiss mice and identification of possible interactions of flavonoids in pro‐ inflammatory proteins. The mice (25‐30g) were divided into 4 groups (n=6): Saline group (NaCl 0.9%), 5‐FU group, Troxerutin group (150mg/kg troxerutin, orally) and Rutin group (300mg/kg rutin, orally). All animals except the Saline group received 5‐ FU at a concentration of 450 mg/kg in the first experimental protocol. To investigate morphological changes, periodic acid Schiff (PAS), toluidine blue, hematoxylin and eosin staining were performed. For the oxidative damage evaluation, the levels of the reduced antioxidant glutathione and the lipid peroxidation product, malondylaldehyde, of duodenal segments were determined. In silico molecular docking assays of the complexes formed between flavonoids (rutin, troxerutin and isoquercitrin) and the COX‐2, TNF‐α and NF‐kB enzymes were performed. The results showed that the antineoplastic 5‐FU promoted oxidative stress, evidenced by a decrease in reduced glutathione (GSH) and an increase in malondialdehyde (MDA) when compared to the saline group (p <0.05). Furthermore, the administration of flavonoids rutin and troxerutin promotes a decrease in MDA levels and an increase in GSH reserves (p <0.05), which culminate in attenuation of the oxidative stress promoted by the antineoplastic agent. The antioxidant effect of flavonoids corroborates the histopathological results, which show that both flavonoids have a significant reversal of antineoplastic‐induced morphological changes (p <0.05), such as reduction of villus height, deepening of the crypts, decrease in goblet cells and increase in mast cells and inflammatory infiltrate. Finally, molecular docking showed that the flavonoids rutin, troxerutin and isoquercitrin show stable binding to the target sites of COX‐2, NF‐kB, TNF‐α, important pro‐inflammatory proteins in inflammatory and ulcerative processes such as intestinal mucositis. It was concluded that the antioxidant effect promoted by flavonoids is one of the protective mechanisms of these natural products of the D. Gardnerian tree to prevent the morphophysiological damage of 5‐FU induced intestinal mucositis.