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Repetitive neuromuscular magnetic stimulation (rNMS) for pediatric headache disorders is feasible, safe, and alleviates headache symptoms. This study assesses muscular effects and factors affecting response to rNMS. A retrospective chart review included children with headaches receiving six rNMS sessions targeting the upper trapezius muscles. Pressure pain thresholds (PPT) were measured before and after rNMS, and at 3-month follow-up (FU). Mean headache frequency, duration, and intensity within the last 3 months were documented. In 20 patients (14.1 ± 2.7 years), PPT significantly increased from pre- to post-treatment (p < 0.001) sustaining until FU. PPT changes significantly differed between primary headache and post-traumatic headache (PTH) (p = 0.019–0.026). Change in headache frequency was significantly higher in patients with than without neck pain (p = 0.032). A total of 60% of patients with neck pain responded to rNMS (≥25%), while 20% of patients without neck pain responded (p = 0.048). 60% of patients receiving rNMS twice a week were responders, while 33% of patients receiving rNMS less or more frequently responded to treatment, respectively. Alleviation of muscular hyperalgesia was demonstrated sustaining for 3 months, which was emphasized in PTH. The rNMS sessions may positively modulate headache symptoms regardless of headache diagnosis. Patients with neck pain profit explicitly well. Two rNMS sessions per week led to the highest reduction in headache frequency.

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