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Background: Esophageal atresia (EA) is a rare congenital malformation of the esophagus. Surgical treatment is required to restore the continuity of the esophagus. This can be performed through thoracotomy. However, an increasing number of hospitals is performing minimal invasive surgery (MIS). In this article, we describe the technique of thoracoscopic repair of EA in neonates in more detail and show the outcome of a patient cohort operated by young pediatric surgeons in training. Methods: Between 2014 and 2019 correction was performed in 64 EA type C patients at the UMC Utrecht, Wilhelmina Children's Hospital, mainly by young pediatric surgeons in training. Results: All patients were corrected through MIS, 3 days after birth. The median operation duration was 181 (127-334) minutes. Nasogastric tube feeding was started on the first postoperative day, and oral feeding 6 days postop. Postoperative complications included leakage (14.1%), stenosis (51.1%), and recurrent tracheoesophageal fistula (7.8%). Conclusion: Thoracoscopic repair of EA can be performed safely, with good outcome and all the benefits of MIS. However, it remains a challenging procedure and should be performed only in pediatric centers with a vast experience in MIS, especially when training young pediatric surgeons. These centers must have access to a multidisciplinary team of neonatologists, pediatric anesthesiologists, surgeons, and ENT specialists to ensure the best possible care in hemodynamic, respiratory, and cerebral monitoring and gastrointestinal and developmental outcome.