Gastrointestinal stromal tumors (GISTs) in the small intestine are relatively rare. We present a case of GIST arising from the small intestine, which could be resected under laparoscopic assistance. A 60-year-old male visited another hospital due to massive anal bleeding. Blood examination showed severe anemia. Although anemia improved after conservative treatment, the bleeding site was not identified and he was referred to our hospital for close examination. Abdominal CT showed a well-defined mass with homogeneous internal density in the left upper abdomen. On abdominal angiography, selective enhancement of the second jejunal artery revealed a tumor stain. Due to suspected GIST in the small intestine, laparoscopic-assisted resection of the jejunum was performed. Histopathological examination demonstrated low-grade malignant GIST. The laparoscopic procedure is considered to be useful as minimally invasive surgery for diagnosis and treatment of selected cases with GISTs in the small intestine.