Ehlers-Danlos syndrome (EDS) is a relatively rare syndrome characterized by excessive stretching of the skin and joints and hemorrhage and increased tissue fragility due to abnormal collagen. Particularly, vascular type EDS has been associated with type III collagen-rich aorta and intestinal tract fragility, owing to which young people are at a risk of spontaneous arterial rupture, aneurysm, aortic dissection, and gastrointestinal perforation. However, there have been few reports regarding gastric submucosal hematoma caused by EDS. Herein, we presented the case of a 29-year-old man who was diagnosed with EDS during his childhood and used to attend another hospital. He visited our hospital after developing epigastralgia and vomiting. The patient presented with pyloric stenosis caused by gastric antrum submucosal hematoma as revealed via abdominal contrast-enhanced computed tomography (CT), esophagogastroduodenoscopy (EGD), and endoscopic ultrasonography. He was admitted and underwent conservative therapy in addition to fasting, drip infusion, and tube feeding. The follow-up CT and EGD revealed hematoma shrinkage, after which he was discharged as no further deterioration was observed. Thus, based on the observed EDS characteristics, an accurate diagnosis is warranted to avoid unnecessary invasive therapy.