Considering the complex pathobiology of oral mucositis, especially in oral cancer patients, the prevention and treatment of oral mucositis in patients undergoing radiotherapy remains an essential and clinically crucial unmet need. The present study aims to investigate and compare the effects of synbiotic mouthwash with normal saline mouthwash on the prevention and control of radiotherapy-induced oral mucositis in oral cancer patients. Double-blind, randomized clinical trial (RCT) performed on 64 oral cancer patients who underwent radiotherapy (IRCT20201106049288N1, registration date: 2020-12-23). Patients were divided randomly into the case (32 subjects) and control (32 subjects) groups. All patients underwent intensity-modulated radiotherapy and received 6000 cGY of radiotherapy in 34 fractions. All patients received the usual treatment for mucositis, but in the case group, synbiotic mouthwash was prescribed and in the control group, normal saline mouthwash was prescribed from a day before the start to the end of radiotherapy treatment. Patients were monitored every session for 6weeks to check the progression, oral involvement severity, and mucositis grade. The case group showed a significant reduction in the oral mucositis severity. The mucositis grade in the case group from the 7th session of oral examination was significantly lower than the control (p < 0.05), and this significant difference persisted until the last session of oral examination. Incidence rates of severe oral mucositis (grade 3) during the treatment period were 11.59% in the case and 36.45% in control (p < 0.001). Synbiotic mouthwash significantly reduces and prevents oral mucositis intensity in oral cancer patients undergoing radiotherapy.