Introduction <p>Intestinal atresia is the complete occlusion of the intestinal lumen at various parts of the intestine. It has the potential to cause intestinal failure. Two mechanisms are suggested: failure of recanalization and/or accidental injury. This case report aims to discuss an exceptionally rare case of congenital total intestinal atresia.</p> Case presentation <p>A 1-day-old male neonate, Tigrian ethnic of Ethiopia born at term, was brought to our hospital with the complaint of repeated vomiting and abdominal distension soon after birth. On examination, he had stable vital signs and a minimally distended abdomen. Abdominal imaging showed features of intestinal obstruction. With a preoperative impression of jejunal atresia, he underwent exploratory laparotomy. The findings were a type IIIa jejunal atresia in addition to an atretic intestine starting from half of the jejunum to the rectum, along with a distended stomach, duodenum, and blind-end jejunum. Decompressive jejunostomy was performed.</p> Conclusion <p>Total intestinal atresia is an extremely rare and fatal condition in our setting. Future investigations are required to examine early prenatal detection for effective intervention and prevention.</p>