Idiopathic portal hypertension (IPH) is a condition of non-cirrhotic portal hypertension without a known cause of liver disease. Obliterative portal venopathy is regarded as the primary lesion, which is responsible for the pre-sinusoidal block of hepatic blood flow leading to the development of IPH. The disease pathogenesis of IPH seems to be heterogeneous, and the pathogenic mechanisms of obliterative portal venopathy have not been fully understood. Owing to the limited understanding of the disease pathogenesis, the treatment of IPH is still largely supportive. Recently, endothelial dysfunction has been documented during the development of portal hypertension, and its contribution to IPH is being analyzed. Endothelial-mesenchymal transition (EndMT) is a phenomenon whereby vascular endothelial cells acquire myofibroblastic features characterized by an ability to express mesenchymal cell products that are related to tissue fibrogenesis. In addition to cardiovascular development, there is increasing evidence showing that EndMT is likely to be involved in a variety of fibrotic diseases, such as cardiac, pulmonary, and renal fibrosis. This article reviews the recent progress in studies of the pathogenic mechanisms of IPH in terms of endothelial dysfunction of portal veins. In particular, the role of EndMT in obliterative portal venopathy of IPH is highlighted and discussed.