INTRODUCTION: Chronic gastrointestinal bleeding in patients with Crohn's disease presents diagnostic challenges. Adult intussusception is rare and typically caused by a pathological lead point, such as a tumor or inflammatory lesion. Lipomas, though benign, can lead to obstruction and bleeding, requiring differentiation from inflammatory causes for appropriate management. CASE PRESENTATION: A 70-year-old male with Crohn's disease and chronic anemia presented with recurrent obscure gastrointestinal bleeding. Initial endoscopy was unremarkable, but capsule endoscopy identified a bleeding jejunal lesion. Double-balloon enteroscopy and imaging confirmed a jejunal lipoma causing intermittent intussusception. Due to persistent anemia, the patient underwent laparoscopic resection, with pathology confirming an ulcerated lipoma. His anemia resolved postoperatively. CONCLUSION: This case underscores the importance of considering structural lesions like lipomas in patients with chronic bleeding and Crohn's disease. A multimodal approach, including advanced imaging and enteroscopy, is crucial for accurate diagnosis and management. Surgical resection remains the preferred treatment for symptomatic small bowel lipomas.