BACKGROUND: Meckel's diverticulum and intestinal duplication malformations are two isolated digestive tract malformations in children. It is uncommon to see cases of both digestive tract malformations occurring at the same time. This report presents a rare case of Meckel's diverticulum complicated with intestinal duplication, highlighting the importance of intraoperative exploration. CASE PRESENTATION: A 5-year-old Han Chinese boy presented with abdominal pain and vomiting. The patient had tenderness in the right lower quadrant of the abdomen. Preoperative imaging suggested Meckel's diverticulum, but intraoperative exploration revealed both Meckel's diverticulum and intestinal duplication. Surgical resection and anastomosis were performed, and histopathology confirmed the diagnosis. The patient was discharged 7 days after surgery. CONCLUSION: Meckel's diverticulum combined with intestinal duplication malformations is rare, and intraoperative exploration is essential in the diagnosis and treatment of surgical disease.