Background Neural tube defects are common group of central nervous system anomalies of complex etiology and major public health importance worldwide. The occurrence of multiple neural tube defects, however, is an extremely rare event and has never been reported in Ethiopia so far. This study gives an insight into how the embryogenesis, management, and postoperative complications of multiple neural tube defects differ from the ordinary single neural tube defects on the basis of up-to-date existing literature. Case presentation This paper highlights a case of an 8 days old female black race Ethiopian neonate who was brought by her mother with the chief complaint of lower back and lower neck swelling since birth. The findings were a 5 × 4 × 5 cm sized ulcerated placode at the mid-lumbosacral area and a 1.5 × 1.5 × 1 cm sized fluctuant, nontender, transilluminating mass with overlying unruptured defect dysplastic skin at the cervicothoracic junction. With a diagnosis of multiple neural tube defects secondary to unruptured cervicothoracic meningocele and ruptured lumbosacral myelomeningocele, single-stage repair of the defects was done with good outcome. Conclusion There is insufficient evidence as to the exact mechanism of development of multiple neural tube defects. Similarly, whether patients with multiple neural tube defects had increased risk of post repair hydrocephalus compared with patients who have single neural tube defect is unknown. Hence, more research on the embryogenesis, management, and long-term outcome of multiple neural tube defects in particular and single neural tube defects in general should be done to better help patients with this costly and crippling problem. Lastly, the practice of folic acid supplementation is very low in resource-limited countries such as Ethiopia and, hence, should be improved.