Ileal atresia, a subtype of intestinal atresia, is one of the well-recognized causes of bowel obstruction in newborns. Prenatal diagnosis of intestinal atresia is very important in its management and outcome. Unfortunately, there are few cases of ileal atresia diagnosed prenatally, so more appropriate diagnoses and management plans are needed. As an associated gastrointestinal malformation with ileal atresia, hypertrophic pyloric stenosis is rarely reported. We report one case of postnatally diagnosed ileal atresia associated with hypertrophic pyloric stenosis which was complicated initially by bowel perforation and later by vomiting due to pyloric obstruction. Vomiting in the postoperative period is a common problem. But, if vomiting continues after the operation for ileal atresia, hypertrophic pyloric stenosis should be considered as a possible cause of medically retractable non-bilious vomiting.