Objective: To investigate the effects of repetitive transcranial magnetic stimulation (rTMS) on cognitive function and serum brain-derived neurotrophic factor (BDNF) in adolescents with depressive disorder (DD). Methods: A total of 104 adolescent DD patients treated in the psychiatric department of the Affiliated Hospital of Wanxi Health Vocational College from January 2019 to March 2021 were randomly divided into experimental group and control group, with 52 cases in each group. All patients received routine drug treatment. The experimental group was treated with low-frequency rTMS of the right dorsolateral prefrontal cortex (DLPFC), and the control group was treated with false stimulation at the same stimulation site, and the observation lasted for 4 weeks. Hamilton Depression Scale-24 (HAMD-24), Montreal Cognitive Assessment Scale (MoCA), connection test-a (TMT-A), serum BDNF level, antidepressant efficacy and adverse reactions were compared between the two groups. Results: After 4 weeks of treatment, HAMD-24 score and TMT-A completion time decreased significantly, and MoCA score and serum BDNF level increased significantly (all P<0.05). After 4 weeks of treatment, the score of HAMD-24 and the completion time of TMT-A in the experimental group were lower than those in the control group, and the reduced score of HAMD-24, the increased value of serum BDNF and the remission rate of DD in the experimental group were higher than those in the control group (all P<0.05). After 4 weeks of treatment, the reduced score of HAMD-24 was positively correlated with the increased value of serum BDNF (r=0.549, P<0.05). There were 3 cases of mild adverse reactions in the experimental group, which improved after appropriate rest. Conclusion: rTMS cannot only effectively alleviate DD symptoms, improve serum BNDF level and DD remission rate, but also improve cognitive function.