“Harlequin effect” may be observed in the watershed region of a patient with pulmonary dysfunction, receiving peripheral veno-arterial extracorporeal membrane oxygenation via the femoral vessels. In such cases, retrograde oxygenated blood from the peripheral inflow cannula converges with the antegrade deoxygenated blood ejected from the left ventricle. This occurs when the left ventricle is ejecting significantly but the recovery of pulmonary function lags behind. Herein, we describe the occurrence of “Harlequin effect” in the setting of central veno-arterial extracorporeal membrane oxygenation that ensues due to the persistence of right ventricular dysfunction in the presence of an interatrial communication. This results in right to left shunting at the atrial level while weaning the patient from extracorporeal life support.