Hereditary protein C deficiency (PCD) is caused by mutation in the PC gene (PROC). The homozygous mutation form of PCD is rare. Furthermore, in Asia, cases of noncirrhotic patients with portal vein thrombosis (PVT) secondary to PCD have been rarely reported. The present study reported the case of a patient with PVT due to hereditary PCD. Of note, the mutation of PROCc.152G>A was observed in the patient of the present study. According to the current literature, there has been no previous report regarding the mutation of this gene in China. The patient suffered abdominal pain for 20 days, which was accompanied by vomiting for 2 days. Multiple ulcers and diverticula in the sigmoid colon, as well as erosive small ulcers throughout the colon, were discovered during a colonoscopy. Abdominal angiography indicated thrombosis of the portal vein and its branches. Furthermore, laboratory parameters indicated a hypercoagulable state with normal PC antigen values but decreased PC activity. The discovery of blood coagulation-related genes suggested that homozygous mutation in PC resulted in an amino acid missense mutation. Anticoagulants were prescribed after a diagnosis of type II hereditary PCD with PVT was made. After 15 days, the blood coagulation function of the patient was restored to normal and the symptoms were substantially alleviated. Hence, the present study expanded the mutation spectrum of PROC in China and reaffirmed the value of anticoagulant therapy in PCD.