We report the case of a 22-year-old man who presented with a 3-day history of watery diarrhea, abdominal pain, and fever. An image of the abdomen showed a heterogeneously echogenic mass lesion in the pelvis. The results of the blood cultures performed on admission showed the presence of Morganella morganii. Computed tomography-guided tube drainage was performed, and a culture of the drained abscess fluid yielded M. morganii growth. Exploratory laparotomy with segmental resection of the jejunum and excision of the tumor was performed. Pathological examination showed a gastrointestinal stromal tumor (GIST). A GIST abscess caused by M. morganii was diagnosed on the basis of radiological, microbiological, and histopathological findings. The possibility of an infected GIST should be considered during the differential diagnosis of patients with suspected abdominal neoplasm and bacteremia.