Background: Colorectal carcinoma (CRC) is a common cause of cancer-related death worldwide. 5-fluorouracil (5-FU), a first-line chemotherapeutic drug in CRC, has several side effects limiting its therapeutic outcomes. Quercetin (QU) is a dietary bioflavonoid with antioxidant and cytotoxic prooxidant properties. Here, we hypothesize that combination treatment with QU and 5-FU can modulate 1,2-dimethylhydrazine (DMH) induced histological and biochemical changes in the colon of Wistar rats. Methods: A Wistar rats CRC model was established and the animals were randomly divided into five groups. Rats in group A received a suspending vehicle. Group B rats received DMH twice a week subcutaneously for 4 weeks. Animals in the other groups (C, D and E) received the same treatment of DMH, along with QU or 5-FU (individually) or combined QU+5-FU treatment. Results: The DMH-treated rats developed adverse histological alterations (aberrant crypt foci, ACF) and biochemical changes (elevated serum CA19-9; reduced tissue levels of enzymatic antioxidants; elevated CDH12 protein expression and decreased SOX7 mRNA levels). Treatment of DMH-treated animals with QU+5-FU (but not with QU or 5-FU, individually) significantly reversed these changes (i.e., suppressed the formation of ACF; decreased the CA19-9 levels; reduced CDH12 protein expression and increased SOX7 mRNA expression). Conclusions: Conclusively, to the best of our knowledge, our study was the first to evaluate the effects of QU+5-FU treatment on the histological and molecular changes following DMH administration in a rat colon model. Our data suggest that combination therapy with QU+5-FU has therapeutic benefits in colon cancer induced by DMH, with potential for translation to spontaneous disease.