Tracheal injury is a rare but highly morbid complication of endotracheal intubation. Recent reviews have advocated conservative management of these injuries without operative intervention. Extracorporeal membrane oxygenation may be a useful tool in non-operative management of tracheal injury in the setting of severe respiratory failure and need for prolonged intubation. We present a morbidly obese 33 year-old-female with H1N1 influenza pneumonia complicated by acute respiratory distress syndrome and bacterial super-infection who sustained a post-intubation tracheal injury. Concomitant tracheal injury and acute lung injury pose a difficult ventilation dilemma. This patient was successfully managed by venovenous extracorporeal membrane oxygenation, high frequency oscillator ventilation, proning position and tube thoracostomy. The venovenous extracorporeal membrane oxygenation and ventilator management were essential for this patient’s recovery.