Congenital short bowel syndrome (SBS) is a rare condition of the newborn, with several reports demonstrating high mortality. A six-week-old boy presented with chronic diarrhea and failure to thrive. An upper gastrointestinal endoscopy showed a straight duodenum, and multiple small bowel biopsies were histologically normal. An upper gastrointestinal series showed malrotation. At laparotomy, the small bowel was 50 cm in length, confirming the diagnosis of congenital SBS. Parenteral nutrition was initiated and enteral feeding with an amino acid-based formula containing long-chain fatty acids was introduced early and gradually advanced. At the last follow-up examination at 24 months, he was thriving on a regular diet, with normal growth and development. Long-term survival of children with congenital SBS is now possible if enteral feeds are introduced early to promote intestinal adaptation, with subsequent weaning off parenteral nutrition.