The pathophysiology of Patau’s syndrome involves the triplication of chromosomes, leading to multiple comorbidities. An omphalocele is characterized by a protrusion of abdominal contents from the base of the umbilical cord through the peritoneum. An omphalomesenteric duct remnant occurs when there is a failure of duct closure that results in a diverticulum extending from the fetal midgut to the yolk sac. While congenital defects rarely occur simultaneously in patients with Patau’s syndrome, this case report describes a newborn with Patau syndrome who presented with both an omphalocele and an omphalomesenteric duct remnant. The newborn exhibited various congenital abnormalities such as coloboma, microphthalmia, broad nasal bridge, cleft lip, cleft palate, low-set ears, systolic murmur, omphalocele, intestinal umbilical fistula (omphalomesenteric continuous vitelointestinal duct remnant), polydactyly, rocker-bottom feet, left-sided clubbed foot, and ruptured myelomeningocele. Imaging revealed additional complications such as a large patent ductus arteriosus, hypoplastic distal arch, markedly dilated right atrium and left ventricle, and cerebellar hypoplasia. Chromosomal analysis confirmed the diagnosis of Patau’s syndrome. Given the untreatable medical condition, the patient was placed under “Do Not Resuscitate,” and palliative care was initiated. The simultaneous appearance of an omphalocele and an omphalomesenteric continuous vitelointestinal duct is rare, and surgical intervention is the standard of care if the patient is deemed suitable for surgery. However, in cases where surgery is not feasible, palliative care is initiated. Regardless of the outcome, genetic counseling is essential and should include a discussion on paternal autonomy, understanding the disorder, suggesting alternative management methods, and making crucial decisions concerning future family care and planning.