Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors in the gastrointestinal (GI) tract, but are the least common of small intestinal malignant neoplasms. While GI bleeding is the most common clinical presentation of GISTs, intussusception and obstruction are uncommon, as GISTs rarely grow into the lumen. We describe an unusual case of a 50-year-old male who presented with intermittent obscure, overt GI bleeding requiring multiple hospital admissions and blood transfusions. His work-up included abdominal CT imaging, small bowel follow-through, gastroscopies, push enteroscopy, colonoscopies, and anterograde and retrograde double-balloon enteroscopies. Complicating his presentation were colonic angiodysplasias and the development of recurrent venous thromboembolism requiring anticoagulation. Within an hour after an apparently uncomplicated colonoscopy, he developed an acute abdomen secondary to a jejunal intussusception, which led to a laparoscopic small bowel resection and the diagnosis of a jejunal GIST. Given his GIST had no high-risk features, ongoing surveillance with abdominal CT imaging was arranged. This case illustrates the complex presentation and diagnostic difficulty of a jejunal GIST causing obscure, overt GI bleeding and this is the first reported case of a jejunal intussusception following colonoscopy. Due to its submucosal location, multiple endoscopic approaches had failed to diagnose the GIST prior to surgery.