Enteric duplication cysts are rare congenital anomalies, with the ileum being the most commonly affected site. The presence of gastric heterotopia within these cysts is uncommon, and the coexistence of melanosis is exceedingly rare. We report a unique case of ileal duplication cyst with both gastric heterotopia and melanosis in a pediatric patient. A 2-year-old male presented with abdominal pain and discomfort lasting for one month. Imaging revealed a well-defined cystic lesion in the right lower abdomen suggestive of an enteric duplication cyst or mesenteric cyst. The child underwent exploratory laparotomy with resection and anastomosis. The resected specimen was sent for histopathological evaluation. Gross examination showed a segment of ileum with an attached cyst measuring 1.5 cm in diameter. The cyst contained serous fluid and pigmented areas. Microscopic examination revealed gastric mucosa with areas of ulceration and inflammation. Numerous melanophages containing coarse melanin pigment were seen in the submucosa and muscularis. The diagnosis of ileal duplication cyst with gastric heterotopia and melanosis was confirmed. This case highlights a rare and unusual histopathological presentation of an ileal duplication cyst. The coexistence of gastric heterotopia and melanosis is extremely uncommon and should be recognized as part of the differential diagnosis in pediatric gastrointestinal anomalies.