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Rhabdomyoma is the most common cardiac tumor in infancy and commonly located in the ventricles causing outflow obstruction or arrhythmias. We report a rare pediatric (7 month old) case of a right atrial rhabdomyoma presenting with severe cyanosis and low cardiac output from significant tricuspid inflow obstruction with right to left shunt across a stretched patent foramen ovale. We present an emergency cardiac surgery for right atrial tumor resection, and the management of separating the patient with failing right ventricle from cardiopulmonary bypass using a Glenn shunt, since extracorporeal membrane oxygenation (ECMO) or nitric oxide was not available.