The endothelium is a monolayer of cells lining the inner of blood and lymphatic vessels. Endothelial cells (ECs) release subtracts that prevent platelet and leukocyte adhesion and aggregation and modulate blood flow, which is essential for the normal function of the vascular system. ECs play indispensable roles in angiogenesis, homeostasis, stimulus or immune response under normal physiological conditions and its dysfunction is closely associated with pathologies such as cancer, diabetes, and pulmonary hypertension. Abnormal EC metabolism, especially fatty acid dysfunctional metabolism, contributes to the leading causes of pulmonary diseases. Expanding the knowledge of ECs’ dysfunctional metabolism in disease could pave a new way for new therapeutic approaches. In this review, we focus on discussing the latest advances in EC fatty acid metabolism in health and disease, with emphasis on its roles in the pathology of pulmonary hypertension (PH).