Neurenteric cysts are rare congenital lesions that are believed to be the result of the split notochord syndrome. We report the clinical case of a 5-year-old boy presenting with vague gastrointestinal symptoms and fatigue, who had undergone resection of a small intestine duplication cyst as a newborn. Computed tomography revealed a mediastinal neurenteric cyst with partial destruction of several thoracic vertebrae. Resection of the tumor proved effective. Recognition of this disorder is important: because of its benign nature, the prognosis after surgical resection can be good. If the diagnosis is made in an early stage, unnecessary progressive destruction of surrounding structures may be prevented.