Endovascular stent graft repair has become a common treatment for complicated Stanford Type B aortic dissection in order to restore true lumen flow and induce false lumen thrombosis. Using computational fluid dynamics, this study reports the differences in flow patterns and wall shear stress distribution in complicated Stanford Type B aortic dissection patients after endovascular stent graft repair. Five patients were included in this study: two having more than 80% false lumen thrombosis (Group 1), while three others had less than 80% false lumen thrombosis (Group 2) within one year following endovascular repair. Group 1 patients had concentrated re-entry tears around the abdominal branches only, while Group 2 patients had re-entry tears that spread along the dissection line. Blood flow inside the false lumen which affected thrombus formation, increased with the number of re-entry tears and when only small amounts of blood that entered the false lumen exited through the branches. In those cases where dissection extended below the abdominal branches (Group 2), patients with fewer re-entry tears and longer distance between the tears had low wall shear stress contributing to thrombosis. This work provides an insight into predicting the development of complete or incomplete false lumen thrombosis and, has implications for patient selection for treatment.