Objective?To investigate the effect of low frequency repetitive transcranial magnetic stimulation (rTMS) on adolescent depression and its effect on working memory and learning ability. Methods?90 patients with adolescent depression in Dongguan Seventh People’s Hospital from January 2018 to December 2020 were selected as the research objects, they were divided into observation group and control group by random number table method,45 cases in each group. Both groups were given routine drug treatment and cognitive behavioral intervention. The observation group was treated with low-frequency rTMS on this basis. The therapeutic effects of the two groups were compared, the working memory and learning ability of the two groups were evaluated by behavior rating inventory of executive function-adult version (BRIEF-A) and wisconsin card sorting test (WCST) before and after treatment. Results?The total effective rate and overall curative effect of the observation group were better than those of the control group (P ＜ 0.05). The behavior management index, metacognitive index and the total score of BRIEF-A in the observation group after treatment were significantly lower than those in the control group and before treatment (P ＜ 0.05). The scores of correct response number and completed classification number in WCST after treatment in the observation group were significantly higher than those in the control group and before treatment(P ＜ 0.05). Conclusion?The low frequency rTMS is effective in adolescent patients with depression, which is helpful to improve their working memory and learning ability.