The role of functional echocardiography in neonatal intensive care unit is rapidly evolving, and increasingly neonatologists are using it in making clinical decisions in sick infants. Functional echocardiography can provide a direct assessment of hemodynamics on bedside, and may be considered as an extension of the clinical examination to evaluate cardiovascular wellbeing in the critically-ill infant. The physiological information may be used in targeting specific intervention based upon the underlying pathophysiology. Functional echocardiography is being used for diagnosis of pulmonary hypertension, patent ductus arteriosus, hemodynamic evaluation, assessment of cardiac function, and recognition of pericardial effusion and cardiac tamponade in the neonatal intensive care setting. Despite of its increasing popularity, there is a paucity of structured training programs for neonatologists to acquire skills in echocardiography. This review article discusses clinical applications of functional echocardiography in the neonatal intensive care unit.