Bronchogenic and other duplication cysts are congenital abnormalities that can present at any age including adulthood years. They are usually asymptomatic and discovered incidentally on radiological imaging of the chest. They are commonly treated by surgical resection. Recently, endobronchial ultrasound has been used to assist in diagnosis when radiologic imaging is not definitive. Endobronchial ultrasound has been used rarely to drain infected cysts, a rare complication of the bronchogenic cyst. We present a unique case of an infected large bronchogenic cyst treated with endobronchial ultrasound drainage combined with conservative medical therapy. We also review the scarce available literature describing such an approach and its potential complications and add recommendations based on our experience in managing these anomalies.