Repetitive transcranial magnetic stimulation (rTMS) has been used as an investigative and therapeutic tool in neuropsychiatry and is advocated as a therapy for the treatment of psychiatric disorders, particularly adult depression. The therapeutic efficacy of current antidepressants applied to children or adolescents is unsatisfactory; thus innovative treatments such as rTMS are in demand. Large-scale clinical studies are required to determine the safety of rTMS for this age group. The present case report describes a 15-year-old female with depression who had seizure and hypomania during the first session of rTMS concomitant to sertraline 100 mg/day orally. The patient continued on this regimen of sertraline therapy but rTMS was not repeated. Subsequent electroencephalogram (EEG) examination detected no abnormalities and no long-term complications were observed. We suggest that rTMS should be used cautiously to treat adolescents with depressive disorders, particularly when used concomitant to antidepressant treatment.