Portal vein thrombosis (PVT) is a rare but serious complication in the decompensated stage of cirrhosis, and recurrent upper gastrointestinal bleeding and refractory ascites can occur in such patients. In decompensated cirrhotic patients, the application of conventional anticoagulant therapy is limited due to severe coagulation disorders, thrombocytopenia, and history of gastrointestinal bleeding.In this study, we sought to investigate the effect of fondaparinux on acute PVT in decompensated cirrhotic patients.Patients were treated with fondaparinux (2.5 mg, q 24 h, subcutaneously) in the region of the umbilicus for conventional liver protection, after a clear diagnosis was made and contraindications such as active bleeding were ruled out. Other anticoagulants and circulation-improving drugs were not administered. Platelet count, prothrombin time, international normalized ratio, D dimer (DD), and liver function were measured. Furthermore, portal vein color Doppler ultrasound was performed every 7 days while patients were treated with fondaparinux and after portal vein recanalization.The portal vein was recanalized in all patients after treatment (P = .018). The decline in DD had a predictive value for portal vein recanalization (P = .018). No side effects such as bleeding or thrombocytopenia occurred in any of the patients (P > .05).Selective factor Xa inhibitor fondaparinux is effective and safe for acute PVT in decompensated cirrhotic patients.