Aim: To study the therapeutic effects of low-frequency repetitive transcranial magnetic stimulation (rTMS) on patients with depression after traumatic brain injury (TBI), and explore its mechanism. Methods: Depressive patients after TBI were evaluated by using the Hamilton rating scale for depression (HAMD), and then the positive results were randomly divided into study group (n = 32) and control group (n = 32). All the patients received routine antidepression drug treatment, besides, patients in the study group were treated with rTMS, and they were stimulated with 60% of the maximum stimulus intensity at the bilateral frontal lobes, 30 times to each side with the frequency of 0.5 Hz, once a day. All the patients were evaluated with HAMD and mini-mental state examination (MMSE) and the concentrations of monoamine neurotransmitters in plasma were examined before and after treatment. Results: The scores of HAMD and MMSE after treatment in the study group were (6 ± 6) and (23 ± 5) points, and those in the control group were (12 ± 8) and (18 ± 5) points. The concentration of 5-hydroxytryptamine(5-HT) after treatment was (1.42 ± 0.37) μmol/L in the treatment group and (1.35 ± 0.36) μmol/L in the control group. The concentrations of noradrenaline (NA) in the study group and control group were (0.41 ± 0.04) μmol/L and (0.35 ± 0.05) μmol/L respectively, and there were significant differences between the two groups (t = 2.316, P = 0.034 8, t = 2.177 4, P = 0.035 6, t = 5.743 6, P = 0.008, t = 6.473 2, P = 0.009). The recent effective rate was 90%, while the long-term effective rate needed further observation. Conclusion: Low-frequency rTMS relieves the depressive symptoms and improves the quality of life in patients with depression after TBI.