Abstract Background Intussusception is the most common intestinal obstruction among infants and young children. Most of the pediatric cases are ileo-cecal, while jejuno-jejunal and ileo-ileal combined contribute only 2.5% of the cases. Case presentation A 5-day-old child presented with recurrent non-bilious vomiting since birth. Physical examination revealed a slightly distended abdomen. A plain radiograph revealed a countable bubble appearance. The initial clinical diagnosis was gastric outlet obstruction. During surgery, we discovered multiple ileo-ileal intussusception associated with duodenal atresia. We manually reduced the intussusceptions and bypassed the duodenal atresia using Kimura’s procedure. We did not find any significant morbidity in the post-operative phase. Conclusion Multiple ileo-ileal intussusception rarely associates with duodenal atresia. In our case report, the intussusceptions might be indirectly caused by duodenal atresia through various pathophysiology. Other unusual findings also supported this suggestion.