This report presents the extremely rare case of an adult patient who presented with peritonitis caused by the perforation of an ileal duplication, associated with a gastrointestinal stromal tumor (GIST) arising within the duplication. A 70-year-old female was admitted to the hospital with lower abdominal pain. Abdominal computed tomography showed free air in the peritoneal cavity. An emergency laparotomy was performed, presuming diffuse peritonitis caused by a perforation of the gastrointestinal tract. The surgical findings showed that the peritonitis was caused by the perforation of an ileal duplication, 90 cm proximal to the ileocecal valve, with an extrinsic tumor protruding from the duplication. A segmental resection of the ileum-including the tumor and ileal duplication-was performed. Histopathology showed that the tumor was composed of spindle-shaped and epithelioid cells. The tumor was immunohistochemically positive for KIT, with a deletion mutation spanning the intron 10-exon 11 boundary. Accordingly, a diagnosis was made of a GIST arising within a duplication of the ileum. Duplications of the alimentary tract are encountered only occasionally in adults. Although quite rare, malignant change should therefore be considered as a possible complication when a solid portion is observed within a duplication of the alimentary tract.