Objective: This study explores the efficacy of Gingival Mesenchymal Stem Cell (GMSC) therapy in preventing and treating patients with chemotherapy-induced AT mucositis. MSC therapy may function in a twofold manner: an immunomodulator to suppress inflammation related tissue injury and a regenerative role to restore epithelial lining, providing a capability for reversing AT mucositis. Methods: In this controlled and randomized study, wild type C57BL/6 mice were administered intraperitoneal (IP) injections of 5-Flurouracil (5-FU), a chemotherapeutic agent, in order to induce mucositis. IP 5-FU was administered at 50 mg/kg/day at regular intervals until mucositis was sufficiently induced. Induction was assessed clinically and subsequently confirmed with the Multi-Photon Microscopy (MPM). Confirmed cases were treated with Phosphate Buffered Saline (PBS) in the control group and with adherent or spheroidal GMSC in the test group. In vivo effects of the GMSCs were mapped using MPM. Mice were humanely euthanized at day 1, 2, 3, 5, and 7 post treatment injection. The whole tongue was then removed from the oral cavity for histological analysis. Results: All of the images illustrated that prior to 5-FU injections, the tongue papillae looked normal, however post 5-FU injections destruction of papillae and surface epithelial layer as well as altered vascularity were discernible. MPM verified that stem cell treatment caused substantial regeneration of the surface epithelium and papillae, as well as restored vascular patterns, especially with the spheroidal GMSC. Conclusion: GMSC therapy offers a potential form of mitigation for patients undergoing cancer therapies.