We treated a 39-year-old Japanese man who was admitted for an abdominal mass. He had had neurofibroma-like skin lesions since childhood. Computed tomography and endoscopic ultrasound results were consistent with a tumor in the small intestine. Although the tumor was undetectable by single-balloon endoscopy, the patient's background and imaging results led us to suspect a gastrointestinal stromal tumor (GIST). He also met the diagnostic criteria for neurofibroma type 1 (NF1). We performed a surgical removal of the tumor, and the biopsy results led to a definitive diagnosis of GIST. Small bowel GISTs should be considered in cases of NF1.