Objective <p>This study aimed to explore the efficacy and safety of <i>Bifidobacterium</i> combined with high-frequency repetitive transcranial magnetic stimulation (rTMS) in treating depression in adolescents.</p> Methods <p>A total of 100 patients were selected and divided into an experimental group (<i>n</i> = 50) and a control group (<i>n</i> = 50) using a random number table. Patients in the experimental group were treated with <i>Bifidobacterium</i> and high-frequency rTMS, and those in the control group were treated with oral escitalopram oxalate. After 8&#xa0;weeks of treatment, the Hamilton Rating Scale for Depression (HAMD-24) score, serum inflammatory factors, neuroendocrine indicators and microRNAs were determined in both groups. The single-blind principle was strictly followed throughout the study.</p> Results <p>The HAMD-24 score after treatment significantly decreased in the experimental group compared with the control group, with a statistically significant difference (<i>p</i> &lt; 0.05). The levels of serum tumour necrosis factor-α, interleukin (IL)-1β and IL-6 also decreased significantly in the experimental group compared with the control group (<i>p</i> &lt; 0.05). Additionally, the elevated levels of dopamine, serotonin and cortisol, including dopamine, 5-hydroxytryptamine and cortisol, was more pronounced in the experimental group than in the control group. The serum levels of miR-16 and miR-195 also showed statistically significant differences (<i>p</i> &lt; 0.05).</p> Conclusion <p><i>Bifidobacterium</i> combined with high-frequency rTMS is effective in the treatment of depression in adolescents with a favourable safety profile, providing references for the clinical treatment of this disease.</p> <p><i>Clinical trial number</i>: ISRCTN16752763 (<a href="https://doi.org/10.1186/ISRCTN16752763">https://doi.org/10.1186/ISRCTN16752763</a>), Date: 19/03/2025.</p>