A 67-year-old man visited our hospital with an enlarging abdominal mass several months after he had first noticed his symptoms. An elastic firm tumor was palpated on the left side of the abdomen upon physical examination. The blood test results were normal. Contrast-enhanced computed tomography of the abdomen revealed a 10-cm-diameter homogeneous low-density cystic tumor located at the dorsal portion of the gastric corpus. Enhancement of a few net-like structures was noted, but most of the lesion was not enhanced. Gastroendoscopy revealed the lesion to be a submucosal tumor with a smooth mucosal surface and no ulceration. Endoscopic ultrasonography showed the tumor arising from the fourth layer of the gastric wall. The tumor was completely resected by laparotomy and partial gastrectomy. It was capsulated and contained serous fluid with little solid tissue. Histologically, there were sparse tumor cells within the myxoid interstitium. Immunostaining results were weakly positive for KIT and CD34-positive accompanied by mast cell infiltration. A platelet-derived growth factor receptor alpha (PDGFRA) exon 18 (D842V) mutation was identified, and the lesion was ultimately diagnosed as myxoid epithelioid gastrointestinal stromal tumor (GIST) of intermediate- and low-risk according to Fletcher's classification and Miettinen's classifications, respectively. GISTs with PDGFRA D842V mutations are reportedly resistant to imatinib, and GISTs originating from the stomach are reportedly less malignant than others. The patient was observed without adjuvant therapy after surgery because of the relatively low risk of metastasis or recurrence and the potential risk of imatinib resistance. No recurrence was observed for ≥5 years after the surgery. We herein report this rare case and describe its clinical characteristics.