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Background Hyperactive dysfunction syndrome (HDS) refers to a constellation of symptoms developing from cranial nerve overactivity caused by neurovascular compression at the root entry or exit zone near the brainstem. Although the combined features of HDS are seen in the elderly, there are no reports of such cases in adolescents, to date. Case presentation A 17-year-old male was diagnosed with right glossopharyngeal neuralgia and treated with microvascular decompression. He experienced new-onset right facial pain later and was diagnosed with right trigeminal neuralgia, which required prompt radiofrequency thermocoagulation of the right mandibular nerve. Follow-up in the third post-treatment year revealed the absence of symptom recurrence. Discussion We report the treatment of a rare case of adolescent-onset combined HDS presenting as trigeminal and glossopharyngeal neuralgia. This report highlights the possibility of combined hyperactive dysfunction syndrome in younger age groups. It is crucial to establish a diagnosis early on for prompt management.