Management of newborn infants with esophageal atresia and tracheoesophageal fistula that require mechanical ventilation is challenging. Without rapid control of the fistula, these patients develop profound respiratory failure and massive distention of the gastrointestinal tract. We present the case of a newborn who upon intubation exhibited respiratory failure and cardiovascular collapse, and in whom traditional intra-operative techniques to gain control of the tracheoesophageal fistula were unsuccessful. We describe a technique that temporarily occludes the gastroesophageal junction, and allows for stabilization of the neonate and definitive repair of the tracheoesophageal fistula.