BACKGROUNDAtlanto-occipital (AO) juxta-articular cysts are positioned within the hypoglossal canal, which houses the hypoglossal nerve. These cysts, whether intraneural or extraneural, can exert localized pressure on the nerve, causing isolated ipsilateral hypoglossal nerve palsy (HNP), an unusual clinical finding. The authors contribute to the scarce literature on this atypical and challenging pathology, reviewing the diagnostic complexities, preoperative indicators, key imaging features, and management strategies.OBSERVATIONSA 55-year-old male presented with tongue deviation, difficulty moving his tongue, and slurring of speech. Physical examination revealed isolated right HNP. MRI showed a lobulated T2 hyperintense lesion with thin rim enhancement at the right hypoglossal canal, extending to the AO joint, suggesting a juxta-articular cyst. CT-guided cyst aspiration decompressed the lesion but yielded no fluid. The patient’s symptoms temporarily improved but then were unchanged over 10 months.LESSONSAO juxta-articular cysts, although rare, should be considered in the differential diagnosis of isolated HNP. High-resolution imaging is crucial for accurate diagnosis. While surgical options exist, conservative management could be appropriate depending on the clinical scenario. CT-guided cyst aspiration can provide temporary relief, but long-term improvement is uncertain. This case emphasizes the link between spinal pathology and cranial nerve dysfunction, underscoring the need for individualized treatment approaches.https://thejns.org/doi/10.3171/CASE24776