Purpose Atypical parafibromin deficient parathyroid tumour is a recently described entity in endocrine pathology. Parafibromin deficiency is often associated with parathyroid carcinoma. However, in the absence of invasive features, atypical parafibromin-deficient neoplasms display distinct morphological characteristics that can lead to a diagnosis of hyperparathyroid jaw tumour (HPT-JT) syndrome. This syndrome is a rare familial cause of primary hyperparathyroidism (PHPT) that requires early recognition and lifelong follow-up to mitigate associated risks. Methods We present the case of a 12-year-old female who presented to Westmead Hospital with hypercalcaemia secondary to primary hyperparathyroidism. The clinical presentation, imaging, surgical management, and histopathological findings are discussed. Emphasis is placed on the investigations required to confirm a diagnosis of HPT-JT syndrome. Results HPTJT syndrome is an exceptionally rare cause of primary hyperparathyroidism, particularly in the paediatric setting. This condition requires lifelong surveillance due to the risk of parathyroid carcinoma, as well as a risk of jaw, renal and uterine tumours. Additionally, atypical parafibromin deficient parathyroid neoplasms have a small malignant potential and require appropriate surgical management. Conclusion This case highlights a rare cause of paediatric primary hyperparathyroidism and contributes to the scarce literature on atypical parafibromin deficient parathyroid neoplasms. The finding of a non-malignant parathyroid tumour with loss of parafibromin expression indicates molecular testing for HPT-JT syndrome. Early diagnosis and appropriate management are essential to mitigate risks and improve long-term outcomes.