The prevalence of depression among adolescents has been significantly increasing in recent years. However, current antidepressants for adolescents have limited safety and efficacy. Acupuncture has been shown to be effective in treating depression in adults, but there is a lack of high-quality evidence for its effect on the treatment of adolescent depression, and the underlying mechanism is still unclear. Therefore, we designed a randomized controlled trial to explore the effectiveness and the therapeutic mechanisms of acupuncture on adolescent depression. This study will be designed as a multi-center, sham and randomized controlled clinical trial. For this purpose, a total of 96 adolescent depression patients diagnosed with moderate and severe depression will be randomly divided into the manual acupuncture group and the sham one, respectively. The two groups received acupuncture treatment 3 times a week for a total course lasting 4 weeks. All patients will be assessed according to the primary outcomes including Beck Depression Inventory-II (BDI-II), Hamilton Depression Rating Scale (HAMD-24) and Zung self-rating depression scale (SDS) at baseline, week 2, 4 and 8. Additionally, the secondary outcomes will be assessed at baseline and week 4, which includes intestinal flora structure, fecal short chain fatty acids (SCFAs) content and serum serotonin (5-HT) level. This study is the first randomized trial of acupuncture treatment of adolescent depression. Trial registrationChinese Clinical Trial Registry, ChiCTR2200064359. Registered on October 4, 2022.