Neurenteric cysts (NCs) are uncommon congenital cystic lesions. Malignantly transformed NCs are extremely rare. The present study reports the case of a recurrent foramen magnum NC with a malignant transformation and reviews 8 previously reported cases. A 58-year-old woman with a 5-month history of occasional headaches, dizziness and vomiting presented to the Beijing Tiantan Hospital (Beijing, China) with palsy of the left cranial IX and X nerves, decreased sensation in the limbs on the right side and an ataxic gait. Magnetic resonance imaging (MRI) scans revealed a cystic mass in the left side of the foramen magnum, positioned anteriolaterally to the medulla oblongata. Surgery using a left suboccipital retrosigmoid approach was performed. The lesion was partially resected and was histopathologically diagnosed as an NC with focal hyperplasia of the epithelial cells. Additional MRI scans that were performed 25 months later revealed a solid lesion posterior to the medullar oblongata. Therefore, surgery using a suboccipital midline approach was performed. The solid lesion was sub-totally removed and was histopathologically diagnosed as a well-differentiated papillary adenocarcinoma. At 1 month post-surgery, the patient's condition worsened, eventually resulting in mortality due to respiratory failure. Based on the findings of the present case and previous literature, strict criteria for malignant-transformed NCs were created. The location distribution of malignant-transformed NCs does not coincide with the location distribution of all NCs, and malignantly transformed NCs usually occur in adult patients and present as atypical radiological features. Surgery is the optimal treatment for malignantly transformed NCs, and the effectiveness of adjuvant therapy requires additional studies.