A male aged in his 30s was referred to our hospital for examination and treatment after an upper gastrointestinal endoscopy revealed extramural compression. Ultrasonography revealed a mass lesion approximately 40 mm in maximum diameter, with a cyst inside the posterior wall of the fornix. The interior was mosaic-like, and part of it was suspected to be continuous with the fourth layer. Following biopsy, a preoperative diagnosis of suspected gastric plexiform angiomyxoid myofibroblastic tumor was made. A laparoscopic partial gastrectomy was performed for both the pathological diagnosis and treatment. A malignant glomus tumor diagnosis was subsequently made based on the results of various immunohistochemical stains. Since then, no tumor recurrence has been observed during follow-ups. Malignant glomus tumors are exceedingly rare; however, they can be locally aggressive and have the potential to metastasize. Further reports and analyses are needed to better understand this disease.