Schizophrenia and major depression disorders, both being of pathological synaptogenesis, are the most common psychiatric disorders worldwide. These diseases, if not treated effectively, may cause suicide and are a serious social and economic challenge. Although schizophrenia and depression can be significantly improved with the second-generation atypical antipsychotics, rising drug resistance has limited their efficacy. Repetitive Transcranial Magnetic Stimulation (rTMS) has appeared to be a promising therapy against severe mental disorders, but it is still controversial primarily due to inadequate evaluation. It is essential to have a reliable biological marker to evaluate and diagnose schizophrenia or depression. Brain-derived neurotrophic factor (BDNF) has appeared to play a critical role in certain neurobiological modifications that may otherwise lead to schizophrenia or depression. Meta-analyses have demonstrated that serum BDNF levels were tightly correlated with the courses of severe schizophrenia and major depression disorders. This article presents a review of BDNF as a neurobiological marker for schizophrenia and depression and for the efficacy of rTMS treatments of these mental diseases.