Pneumatosis intestinalis is an unusual intestinal pathology that is characterized by the presence of gas within the intestinal wall, usually in the mucosa or submucosa of the small or large intestine. Sunitinib is a small molecule that inhibits multiple receptor tyrosine kinases such as KIT, vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF). It is used as second-line therapy for patients with imatinib-resistant gastrointestinal stromal tumors (GIST). We report here a 61-year-old male patient diagnosed with recurrent GIST complicated by massive peritoneal metastasis involving the small intestine, with resistance to imatinib. Following rapid response to sunitinib treatment, pneumatosis intestinalis of the small intestine occurred and led to perforation at a previous anastomotic site. In conclusion, the possibility of pneumatosis intestinalis and intestinal perforation associated with rapid response should be considered during antiangiogenic therapy in patients with malignancies involving the gastrointestinal tract.