The aim of the present study was to assess the safety and effectiveness of high-frequency repetitive transcranial magnetic stimulation (rTMS) in pregnant patients with depression. Thirty depressed pregnant patients received rTMS over the left prefrontal cortex for 6 days in a week, from Monday to Saturday for 3 weeks. The rTMS intensity was set at 100% of the motor threshold. A 25-Hz stimulation with a duration of 2 s was delivered 20 times with 30-s intervals. A session comprised 1,000 magnetic pulses. Depression was rated using the 17-item Hamilton depression rating scale (HAMD) before and after treatment. Response was defined as a 50% reduction of the HAMD score. Patients with HAMD scores less than 8 were considered to be in remission. The mean HAMD score for the study group decreased from 26.77 ± 5.58 to 13.03 ± 6.93 (p < 0.001) after 18 sessions of rTMS. After the treatment period, 41.4% of the study group demonstrated significant mood improvements as indexed by a reduction of more than 50% on the HAMD score. In addition, 20.7% attained remission (HAMD score < 8), 34.5% achieved a partial response, and 3.4% had worsening in HAMD scores at the end of treatment. Treatment was well tolerated, and no significant adverse effects were reported. rTMS was well tolerated and found to be statistically and clinically effective in pregnant patients with treatment-resistant depression. This study contributed to the existing evidence of the antidepressant effect of rTMS in the treatment of depression in pregnancy.