Catastrophic antiphospholipid syndrome (CAPS) is a multisystem autoimmune disease with widespread thrombotic events. In this case report, we present a young man with primary antiphospholipid syndrome (PAPS) admitted to the hospital with abdominal pain and vomiting. Abdominal computed tomography showed pneumoperitoneum and acute explorative laparotomy revealed small intestinal necrosis indicating small vessel thrombosis without involvement of large intestine. “Triple therapy” was initiated after surgery and the patient was treated in an intensive care unit for 72 days before being discharged to a rehabilitation clinic. A review of the literature regarding CAPS affecting small intestine shows it is extremely rare and may be associated with higher mortality.