Congenital eventration of the diaphragm is a rare disorder, the perioperative management of which is challenging. The introduction of thoracoscopic repair of these defects has considerably reduced the perioperative morbidity and mortality in these patients. In spite of the advantages of thoracoscopy which include smaller chest incisions, reduced postoperative pain, and more rapid postoperative recovery compared with thoracotomy, it is still inherent with complications unique to it. A clear understanding of the pathophysiologic changes, potential complications and institution of appropriate monitoring and good planning is essential for the safe conduct of thoracoscopic procedures in neonates. We describe the anesthetic management of staged thoracoscopic repair of bilateral congenital eventration of the diaphragm in a neonate.