The Fontan operation is considered the final palliation for patients who have a structurally or functionally univentricular heart, that is a condition in which the heart is unable to function in a state where there are two pumps: one for the left side of the heart that pumps the oxygenated blood into the systemic circulation and another for the right side of the heart that pumps blood into the pulmonary circulation (lungs). Although the Fontan operation creates an abnormal physiological environment by dispensing away with the right-sided pump, it has proved to be an important surgical tool to relieve cyanosis and improve the functional capacity of patients who were previously doomed to die. Understandably, it has been studied and evaluated critically and there are constant endeavors to make it better. Engineering and medicine can forge an important partnership in making this operation better. In this review the basic aspects of this operation are discussed along with the role of fluid dynamics to modify this operation as well as help in designing pumps to add energy to this circuit for better long-term outcomes.