Adolescent depression is mainly characterized by impaired emotional regulation, motivational drive and cognitive control functions. Such abnormalities often reflect an imbalance among multiple neurofunctional systems. Abnormal connections in related brain regions, such as the dorsolateral prefrontal cortex (DLPFC), the default mode network (DMN), and the reward pathway, may be closely related to its core symptoms. The existing treatment methods have many shortcomings, such as slow onset of action, poor treatment compliance and large individual differences in therapeutic effects. Transcranial magnetic stimulation (TMS) has attracted much attention in the treatment of adolescent depression in recent years. Targeting the left dorsolateral prefrontal cortex (LDLPFC) as the core site of intervention, this approach modulates the balance among distinct neural functional systems. Currently, accelerated TMS (aTMS) has shown certain efficacy in shortening the onset latency, but its long-term therapeutic outcomes remain to be further observed. Neuroimaging techniques elucidate potential mechanisms underlying the therapeutic effects of TMS, primarily attributed to the reorganization of functional connectivity patterns in key brain regions. This review aims to systematically sort out the research related to adolescent depression, comprehensively evaluate the efficacy and safety of current studies, and thereby provide references for individualized treatment.