Background Oral mucositis, a common complication of several different anticancer therapies, causes significant morbidity in cancer patients. It is characterized by the destruction of the mucosa throughout the gastrointestinal tract including the oral cavity. Limited data exist regarding the treatment of established oral mucositis with oral mucoadhesive hydrogel (MuGard) or supersaturated calcium phosphate oral rise (Caphosol) compared to standard topical therapies. Objectives To evaluate the effects of MuGard and Caphosol compared to standard topical therapy in the treatment of established oral mucositis. Methods A retrospective chart review was performed including adults receiving MuGard, Caphosol, and/or standard topical therapy for the treatment of established oral mucositis while admitted to a community teaching hospital. A post hoc propensity score was used to match patients receiving newer agents (Mugard/Caphosol) to those receiving standard topical therapy (ST). Results One hundred and forty-seven patients were included for analysis (125 ST, 15 MuGard, 7 Caphosol). From this population, 14 patients in each group were matched. The primary endpoint of median change in average daily pain score at days 3 and 7, compared to baseline, demonstrated no difference between matched groups at day 3 (ST 0, MuGard/Caphosol 0.18, p = 0.830) or day 7 (ST 0, MuGard/Caphosol 0.8, p = 0.494). No differences were noted between groups in opioid usage, oral mucositis symptom duration or progression, or incidence of documented infection. Conclusion MuGard and Caphosol did not demonstrate any benefits compared to standard topical therapy at reducing pain scores or increasing mucosal recovery in the treatment of oral mucositis.