Background: Esophageal atresia (EA) is a rare congenital malformation of the foregut, most commonly presenting in association with tracheoesophageal fistula (TEF). Advances in neonatal surgical techniques and intensive care have significantly improved survival rates over recent decades. However, short- and long-term respiratory morbidity remains prevalent, substantially impacting patients’ quality of life. Methods: This is a retrospective single-center case series of pediatric patients with repaired EA, with emphasis on the spectrum of pulmonary complications and their clinical management. Six patients with repaired type C EA with TEF and associated respiratory complications were included. All patients were admitted between 2018 and 2026 to the Third Pediatric Clinic, Clinical Hospital for Pediatric Emergencies, Cluj-Napoca, Romania, for the management of respiratory pathology. Results: Tracheomalacia was identified in all six patients, and each had experienced at least one episode of lower respiratory tract infection. Reactive airway disease meeting diagnostic criteria for asthma was documented in two patients. One case raised clinical suspicion for a residual or recurrent tracheoesophageal fistula, warranting further diagnostic workup. Gastroesophageal reflux (GER) was present in all patients. Protein-energy malnutrition was identified in two patients (30% of the cohort). Conclusions: Surgically repaired EA is frequently associated with considerable chronic respiratory and gastrointestinal morbidity. A structured multidisciplinary approach, including pediatric pulmonology, gastroenterology, surgery and nutrition, alongside systematic long-term follow-up, is essential to optimize outcomes and quality of life in this vulnerable patient population.