The frequency rate of esophageal anastomosis leaks after thoracoscopic correction of esophageal atresia (EA) in the current literature is reported as 5.6%–24.7% and a conversion rate of 2%–53%. The objective of this retrospective study was to examine the characteristics of EA and analysis of the safety and efficacy of EA repair with the use of the thoracoscopic approach in a single academic center, as well as risk factors analysis in the context of short-term and mid-term follow-up status. A retrospective analysis of the management of all consecutive newborns affected by EA hospitalized in our department over a period between 2013 and 2022, including preoperative, perioperative, and postoperative management, together with the outcome, complications and long-term follow-up status was performed. A total of 38 patients with a median birth weight of 2,570 g (range; 1,020–3,880) were treated over the study period, including 30/38 (78.9%) with additional congenital anomalies. Overall, 30 patients underwent primary anastomosis of the esophagus and eight underwent a multistaged procedure, with or without an initial ligation of the tracheoesophageal fistula and delayed primary anastomosis. Overall survival for all patients was 0.894 ± 0.050, with a median follow-up of 4.5 years. We noted neither anastomotic leaks nor conversions to open technique in our cohort. Implementation of vancomycin prophylaxis was successful in preventing postoperative central venous access-related infectious complications. At the end of the follow-up, 85% of patients have a Lansky performance score ≥80. Risk factors analysis for length of hospitalization, overall survival, Lansky performance status, and neurological impairment were analyzed. In conclusion, we have found that the outcome of thoracoscopic repair of EA in terms of surgery-dependent morbidity (anastomosis leakage, conversion rate to open surgery), provides benefit to those previously reported in the literature, regardless of the prognostic criteria of the classification system.