Paroxysmal nocturnal hemoglobinuria (PNH) is associated with severe end-organ damage and a high risk of thrombosis. Budd-Chiari syndrome, which develops after thrombotic occlusion of major hepatic blood vessels, is relatively common in PNH and has been associated with increased mortality. We report the case of a 46-year-old male with PNH who presented with Budd-Chiari syndrome associated with portal cavernoma, portal hypertension and hypersplenism. In September 2010, the patient suffered gastrointestinal bleeding, hematuria, and elevated plasma lactate dehydrogenase; he started eculizumab therapy with a good response. In October 2012, he developed upper gastrointestinal variceal bleeding and a splenorenal shunt was placed. At the time of writing, the patient remains stable and eculizumab continues to be effective. There is limited data on the use of eculizumab for prevention of hemolysis and its consequences in PNH patients undergoing surgery. Our findings provide evidence for the efficacy and safety of eculizumab in this setting.