Background <p>Adolescent patients with major depressive disorders (MDD) frequently co-occur with headache, contributing to substantial disease burden and social functional impairment. Repetitive transcranial magnetic stimulation (rTMS) has been supported for MDD and pain conditions, but clinical evidence for a combined affect and pain network targeting strategy in comorbid phenotypes remains limited.</p> Case presentation <p>A 16-year-old male student presented with a 2-year history of depression accompanied by paroxysmal headache. We administered a dual-target rTMS protocol targeting the dorsolateral prefrontal cortex and primary motor cortex. After 2 weeks of treatment (40 sessions), the patient’s depressive and headache symptoms improved significantly.</p> Conclusions <p>This case suggests that an intensified dual-target rTMS approach engaging both affect regulation and pain modulation targets may be feasible for adolescents with comorbid depression and headache. Prospective studies are needed to determine optimal parameters, durability, and safety.</p> Clinical trial number <p>Not applicable.</p>