Background and Objectives: Duodenal atresia and stenosis are common causes of intestinal obstruction. Associated anomalies significantly influence early postoperative mortality, while postoperative complications impact long-term survival. Materials and Methods: Over a 13-year period from January 2010 to August 2023, a total of 74 infants and children with congenital duodenal obstruction were treated at “Grigore Alexandrescu” Children’s Emergency Hospital and met the inclusion criteria. All patients diagnosed with duodenal obstruction (both instrinsic and extrinsic causes) were included. Analysed data included congenital anomalies, Apgar scores, birth weights, surgical techniques, and complications. Results: The associated anomalies included cardiac (n = 33), Down syndrome (n = 13), neurological (n = 11), pulmonary (n = 7), renal (n = 4), skeletal (n = 1), and gastrointestinal and hepatobiliopancreatic anomalies (n = 25). In total, 12 patients experienced perioperative ventilation problems. Early postoperative complications (within 30 days) occurred in 21 patients, while 6 had late postoperative complications (after 30 days). Among non-surgical complications, we noted ventilation problems, sepsis (n = 7), and pneumothorax (n = 1). Surgical complications included adhesive bowel obstruction (n = 7), incisional hernia (n = 3), peritonitis (n = 3), dysfunctional duodenoduodenostomy or duodenojejunostomy (n = 3), pneumoperitoneum (n = 5), enteric fistula (n = 3), and volvulus (n = 4). Conclusions: Surprisingly, this retrospective study revealed that an Apgar score below 8, along with neurological and pulmonary abnormalities, is associated with postoperative complications. Conversely, other congenital anomalies, low birth weight, and age at admission do not serve as prognostic factors.