Background: Ulcerative colitis (UC), a form of inflammatory bowel disease (IBD), increases the risk of colorectal cancer. This study investigates the potential of conditioned medium from mesenchymal stem cells (CMm) treated with 17‐beta‐estradiol (E2) to enhance colon regeneration in UC‐affected rats. Methods: Bone marrow‐derived MSCs from male Wistar rats were cultured with 100 nM E2 for 24 h. UC was induced in three groups: colitis (C), mesenchymal stem cells (MSC), and MSCs + estradiol (MSC + E2). Each group received intraperitoneal injections of 200 μL CMm derived from 2 × 106 cells or E2‐treated CMm three times postinduction. The study evaluated disease activity index (DAI), myeloperoxidase (MPO) levels, nitric oxide (NO), and pro‐inflammatory cytokines (TNF‐α, IL‐1β, IL‐6) in colon tissues, alongside histopathological assessments. Results: Results showed significant improvements in DAI and reductions in MPO, NO, and cytokine levels in MSC and MSC + E2 groups compared to the C group. Histopathological analysis revealed enhanced colon tissue regeneration in these groups. Conclusions: These findings suggest that CMm, particularly with E2, may facilitate colonic healing and mitigate inflammation in UC.