We report the case of a 40-year-old woman with a severe factor XI (FXI) deficiency who died from a stroke due to bilateral internal carotid arteries occlusion after a laparoscopic gastric bypass (bariatric surgery). This stroke was probably secondary to a pulmonary embolism with a paradoxical embolism through a previously unknown foramen ovale. This woman who had one severe episode of bleeding before the bypass received for the intervention a single infusion of 27 U/kg of FXI concentrate. A careful evaluation of the bleeding and thrombotic risk was performed before surgery, and despite all preventive measures, this tragic event occurred. The aim of this report is to alert medical teams to carefully balance the benefit-risk of such an intervention in a patient with a severe FXI deficiency.