Introduction Gastrointestinal clear cell sarcoma is extremely rare gastrointestinal tumour with aggressive cancer with high risk of local recurrence and distant metastasis. There have only been 63 reported cases to date during the literature review. Due to its limited cases, currently there is no recommended protocol for diagnosis, staging, treatment, and surveillance for these patients. Presentation We would like to present a case of 56-year-old woman who presented with acute abdominal pain and small bowel obstruction. Computed tomography confirmed a small bowel obstruction secondary to soft tissue mass (3.4cm in length) in mid small bowel. She was managed with laparotomy and wide local resection of the small intestine including regional lymph node, liver biopsy and primary anastomosis. Histology was consistent with gastrointestinal clear cell sarcoma/ malignant gastrointestinal neuroectodermal tumour. There were no involvement of 20 mesenteric lymph node in the specimen. Patient had uneventful recovery postoperatively and discharged after 6 days. She is currently disease free and being closely followed by surgical team at the Prince Charles Hospital. Conclusion Gastrointestinal clear cell sarcoma can present with very vague abdominal symptoms and mostly presented to Emergency with bowel obstruction. Wide local excision is the current gold standard treatment for this condition but further understanding to the pathogenesis and genetic mutation will benefit in developing protocol for prognosticating, follow up and surveillance.