Reported herein is a gastrointestinal stromal tumor (GIST) that exhibited a hemangiopericytoma (HPC)-like histological pattern. Such a morphological variant of GIST has not been described previously. A 57-year-old woman presented with bloody stools. On upper digestive tract endoscopy a submucosal tumor of diameter 2 cm was detected at the duodenal bulb, and enucleated. Grossly, the tumor was well-circumscribed, grayish to whitish, and solid, and its central portion was ulcerated. Histology indicated round to fusiform tumor cells that had proliferated around branching vessels that had a staghorn configuration. Immunohistochemistry showed that the tumor cells were diffusely positive for vimentin and KIT; partially positive for CD34 and muscle actin; and negative for alpha-smooth muscle actin. On mutation analysis a 42 bp deletion was found from codons 560 to 573 of exon 11 of the KIT gene, which is a mutational hot spot of GIST. In diagnosis of gastrointestinal tract tumors with an HPC-like histological pattern, pathologists should consider the possibility of GIST.