To explore the efficacy and safety of right-sided low-frequency repetitive transcranial magnetic stimulation (rTMS) in treating depression comorbid with anxiety in elderly patients. Methods: A total of 72 elderly patients with depression comorbid with anxiety, hospitalized in the Department of Psychiatry of Liyuan Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology from January 2021 to June 2021, were selected and randomly divided into a control group (35 cases) and a low-frequency group (37 cases) using a random number table. Both groups received antidepressant medication. Additionally, the low-frequency group was treated with rTMS (1.0 Hz) on the right dorsolateral prefrontal cortex, 20 minutes per session, once daily, five times per week, for a total of 20 sessions over 4 weeks. The control group received sham stimulation with the same duration and frequency. The Hamilton Depression Rating Scale-24 (HAMD-24) and the Hamilton Anxiety Rating Scale-14 (HAMA-14) were used to evaluate anxiety and depression symptoms and treatment efficacy at baseline and at the end of weeks 1, 2, 3, 4, 6, and 8. Adverse reactions were recorded, and repeated measures ANOVA was used to compare the scores of anxiety and depression between the two groups at different time points. Results: The main effects of time, group, and time-group interaction for HAMD-24 and HAMA-14 scores were statistically significant (P<0.05). Further analysis showed that HAMD-24 scores in both groups were significantly lower than baseline at weeks 1, 2, 3, 4, 6, and 8 (P<0.01). There was no significant difference in HAMD-24 scores between the two groups at weeks 1, 2, 3, and 4 (P>0.05), but the low-frequency group had significantly lower HAMD-24 scores than the control group at week 6 (P<0.01) and week 8 (P<0.05). For HAMA-14 scores, both groups showed significant reductions compared to baseline at weeks 1, 2, 3, 4, 6, and week 8 (P<0.01). The low-frequency group had significantly lower HAMA-14 scores than the control group at weeks 1 and 2 (P<0.05) and at weeks 3, 4, 6, and 8 (P<0.01). After 4 weeks of treatment, the overall response rate in the low-frequency group was higher than that in the control group (P<0.05). After 6 weeks, the marked improvement rate in the low-frequency group was significantly higher (P<0.05), but there was no significant difference in marked improvement rates between the two groups after 8 weeks (P>0.05). No severe adverse reactions were observed in either group. Conclusion: Combined antidepressant and right-sided rTMS therapy effectively alleviates both depressive and anxiety symptoms in elderly patients with comorbid depression and anxiety, demonstrating superiority to antidepressant medication alone while maintaining a favorable safety profile.