Introduction: Malignant gastrointestinal neuroectodermal tumor (GNET), previously known as clear cell sarcoma-like tumor of the gastrointestinal tract, is an extremely rare and aggressive mesenchymal neoplasm characterized by high rates of recurrence, metastases, and mortality. Currently, there are no standardized guidelines for therapy. Case Presentation: We present a case of GNET in a 32-year-old male with a history of lymphoma and ulcerative colitis (UC), who also had synchronous multiple liver metastasis. To our knowledge, this is the first documented case of GNET in a patient with inflammatory bowel disease. Conclusion: The narrow time frame in which UC and GNET were diagnosed warrants further investigation into their potential relationship.