We report a rare case of late complication of a complex intestinal malformation. At day 1 of life, a baby girl underwent resection of an atretic jejunal segment, associated with an enteric duplication harboring foci of gastric and duodenal heterotopia. After an asymptomatic period of 19 years, the patient presented with acute bowel obstruction. Recurrence of the jejunal occlusion at the previous anastomotic site was caused by mucosa hyperplasia in association with heterotopic gastric and duodenal tissue. A Wnt/β-catenin pathway deregulation was hypothesized but not confirmed by CTNNB1 exon 3 mutation analysis. This case illustrates a rare association of 3 pathologies—namely, intestinal atresia, enteric duplication, and heterotopia, with a late-occurring acute complication.