Introduction: Neuroendocrine tumors (NET) within tailgut cysts (TC) are usually seen in middle-aged females. A 14 year-old boy who underwent surgical excision of NET within TC is presented to discuss the clinical features, diagnosis and treatment options. Case report: A 14-year-old boy with rectal bleeding and constipation had a 5 x 4 cm mass detected upon rectal examination. The cystic mass was totally excised. The histopathological evaluation revealed a low-grade NET within mucularis layer of the cyst showing a positive immunhistochemical staining for cytokeratin and synaptophysin. Conclusion: Although, the malignant transition of TC is commonly observed in middle age females, males and children can also be affected. This is first report of a pediatric TC with malignant transformation. Total surgical excision of cysts is mandatory for local control of the disease and chemotherapy should be reserved for the patients who have positive surgical margins.