Background: Patients with congenital heart disease can associate malformations. The most frequent complications are those related to the airways, which produce prolonged cardiovascular postoperative. Objectives: Describe pathology, bronchoscopy indications, and findings in patients with heart pathology and persistent breath failure to improve prognosis and determine an early treatment. Methods: Retrospective descriptive study of bronchoscopies performed during 24 years in pediatric patients with congenital heart disease with surgery indication and persistent respiratory symptomatology. Results: We performed 199 fibrobronchoscopies in 144 patients, with an average of 1.4 fibrobronchoscopies per patient. A total of 58% were male. The mean age was 27.5 months (5 days–13 years). Valvular disease was the most frequent congenital heart disease, followed by the transposition of large vessels. The most frequent indications were stridor (42.7%) and persistent atelectasis (24.6%), followed by extubation failure (12.4%) and pump output (6.2%). The majority of the findings were found in the upper airway (56%), with a clear predominance of malacias (32%), while in the lower airway, extrinsic compression was highlighted (42%). Conclusions: Flexible fiberoptic bronchoscopy is a useful and rapid method for the diagnosis of airway malformations associated with congenital heart diseases that may have a relevant role in its management and prognosis.