Meckel's diverticulum is a congenital defect in the small intestine that often contains ectopic gastric mucosa and causes painless intestinal bleeding, especially in children and young people. Gastrointestinal stromal tumors (GIST) are mesenchymal tumors of Cajal cells that occur mainly in middle-aged and elderly people. Both conditions can be found in the small intestine, cause bleeding, and have similar imaging features, making it difficult to differentiate. In a 17-year-old female patient with recurrent melena, abdominal pain, and anemia, CT enterography showed a 0.9 cm × 1.8 cm nodular lesion in the ileum with homogeneous enhancement, suggestive of GIST. The previous endoscopy revealed only chronic gastritis and colitis. After laparoscopic resection, pathology confirmed Meckel's diverticulum with an ectopic fundic gland. The case highlights the diagnostic difficulties and the importance of histology in differentiating it from GIST. It provides guidance for similar cases to avoid misdiagnosis.