BACKGROUND Thrombosed intracranial aneurysms are rare in pediatric populations and pose significant diagnostic challenges due to their atypical imaging features, which often mimic neoplasms. These lesions can present with mass effect, contrast enhancement, and calcifications, leading to potential misdiagnosis and inappropriate management. Accurate differentiation through advanced imaging is essential to prevent surgical complications and ensure optimal outcomes. OBSERVATIONS The authors describe the case of a 15-year-old boy with severe acute headaches and an MRI finding of a contrast-enhancing lesion in the left cerebellar tonsil abutting the medulla oblongata, suggestive of a neoplasm. Neurological examination was normal, and there was no significant medical history. Despite negative angiographic findings, the unclear etiology warranted surgical intervention. A median suboccipital craniotomy revealed a capsule-like lesion with arterial feeders from the posterior inferior cerebellar artery. Complete resection was achieved, and histopathology confirmed a thrombosed aneurysm. Postoperative recovery was uneventful, and 1-year follow-up showed full symptom resolution without recurrence. LESSONS This case highlights the importance of considering thrombosed aneurysms in pediatric patients with atypical intracranial lesions. Multidisciplinary collaboration and advanced imaging are crucial for accurate diagnosis and effective management. Documenting such cases enhances understanding, refines diagnostic strategies, and improves patient care. https://thejns.org/doi/10.3171/CASE2592