This study aimed to investigate the radioprotective effect of melatonin (MLT) on brain damage in rats exposed to low and high dose rate radiotherapy. The dose rates of 10 MV photon beams used in the study were 600 MU/min and 2400 MU/min for low dose rate radiotherapy (LDR_RT) and high dose rate radiotherapy (HDR_RT), respectively. A total of 46 female Wistar albino rats aged between 8 and 12 weeks were divided in 6 groups. These groups were control, MLT, LDR_RT, HDR_RT, LDR_RT plus MLT and HDR_RT plus MLT, respectively. Rats in the radiation group received 16 Gy single dose whole body radiotherapy. Rats in the LDR_RT plus MLT and HDR_RT plus MLT groups received 10 mg/kg melatonin by intraperitoneal injection 15 min before radiotherapy. The rats were sacrificed 48 h after radiotherapy. Biochemical and histopathological methods analyzed radiation damage in rats. There was a statistically significant difference between the LDR_RT and HDR_RT radiation groups and the control group in terms of biochemical and histopathological parameters (p < 0.05). In the groups that received only LDR_RT and HDR_RT, the moderate neuro-degeneration scores were 1 and 4, respectively, while the moderate neuro-degeneration scores were 0 and 2 when MLT was applied to these groups. Superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT) enzymes were decreased due to radiotherapy, whereas these enzymes were improved in MLT-treated groups. In conclusion, melatonin was found to be effective as a radioprotective agent in the prevention of brain damage caused by exposure to 10 MV photon radiation at dose rates of 600 MU/min and 2400 MU/min.