Introduction: Esophageal atresia with tracheoesophageal fistula (EA/TEF), anorectal malformation (ARM), and pyloric atresia (PA) are rare congenital anomalies. Their simultaneous occurrence, especially in association with complex cardiac defects such as double outlet right ventricle (DORV), is exceedingly rare. Case presentation: A male neonate was delivered at 33 weeks of gestation via emergency cesarean section due to labor dystocia. Prenatal ultrasound had only identified cardiac anomalies. At birth, the 2000-gram infant presented with respiratory distress. Clinical examination revealed excessive salivation, absence of an anal opening with no visible perineal fistula, and inability to pass an orogastric tube. Chest and abdominal radiographs demonstrated the orogastric tube coiled in the upper esophageal pouch and a single dilated gastric bubble without distal bowel gas, consistent with EA/TEF and suggestive of proximal intestinal obstruction. Echocardiography confirmed the presence of DORV. A right thoracotomy confirmed EA with a distal tracheoesophageal fistula, which was ligated. Given the neonate’s hemodynamic instability, an esophageal anastomosis was deferred, and a staged approach was chosen, with cervical esophagostomy and feeding gastrostomy. During laparotomy, pyloric atresia with complete discontinuity between the stomach and duodenum was identified and managed with a gastro-duodenostomy. A colostomy was also performed for the high-type ARM. Despite initial postoperative stabilization, the infant deteriorated and died on day 15 from sepsis, persistent hypotension, and multi-organ failure. Conclusion: Although rare, patients with EA/TEF or ARM may present with associated pyloric atresia and complex cardiac anomalies. Early recognition and multidisciplinary approach are crucial for management of such challenging neonatal presentations.