We report the first successful use of venovenous extracorporeal membrane oxygenation (ECMO) for refractory respiratory failure in an infant with DiGeorge anomaly, following thymus transplantation. A 23-month-old female with complete immune-incompetent DiGeorge anomaly 65 days after allogenic thymus transplantation was treated in our pediatric intensive care unit for acute respiratory failure secondary to bacterial sepsis. She subsequently developed acute hypercarbic respiratory failure unresponsive to conventional medical therapy. She was successfully managed with venovenous ECMO for 4 days, with complete resolution of her respiratory symptoms. This case demonstrates the complex decision making process regarding initiation of ECMO in patients with severe immunodeficiency.