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Primary amenorrhoea is defined as the absence of menarche by 15 years of age in individuals with normal secondary sexual characteristics and is most commonly due to constitutional delay, gonadal dysgenesis or outflow tract abnormalities. We describe an adolescent female who presented with isolated primary amenorrhoea despite normal pubertal onset and progression and no neurological symptoms. Biochemical evaluation demonstrated a central hypothalamic–pituitary pattern of hypogonadism, prompting neuroimaging. MRI revealed a large intraventricular mass causing obstructive hydrocephalus with compression of the hypothalamic–pituitary axis, alongside multifocal intracranial disease and spinal drop metastases. Integrated multidisciplinary assessment confirmed rosette-forming glioneuronal tumour, a rare central nervous system neoplasm. Management required combined neurosurgical and endocrine input, including cerebrospinal fluid diversion, subtotal tumour debulking and proton beam craniospinal irradiation. This case highlights that central nervous system pathology should be considered in unexplained primary amenorrhoea, even in the absence of neurological symptoms.