Introduction: The current literature lacks a comprehensive investigation into the use of flexible bronchoscopy (FB) in the treatment of childhood atelectasis. Methods: In this retrospective study, the data of pediatric patients who were diagnosed with atelectasis and underwent FB for diagnostic and therapeutic purposes in our center from January 1, 2017 to December 31, 2022 were retracted from medical records. The study aimed to assess the effectiveness of FB in diagnosing and treating atelectasis in children, identifying the appropriate patient population and the optimal timing for intervention. Results: A total of 108 children, with a median age of 4.9 years (14 days-18 years), underwent FB. At the time atelectasis was detected, at least one underlying disease was present in 62% of the patients. Based on the macroscopic and microscopic FB findings, 86.1% of the patients received a new diagnosis, and 83.3% of the patients were prescribed additional new treatments. At the last outpatient visit, complete resolution of the atelectasis was observed in 40.8% of patients, while 31.4% showed no resolution. The duration from the diagnosis of atelectasis to FB was shorter in patients with partial or complete resolution. Patients without additional radiological abnormalities or scoliosis had higher resolution rates, while those with congenital cardiac diseases, immunodeficiency, or primary ciliary dyskinesia had lower rates. Conclusion: Children with atelectasis who do not respond to conventional treatments within three weeks may undergo FB. Delayed FB contributes to failure in resolving atelectasis, prolonged recovery times, and increased recurrence rates, particularly in patients with underlying diseases.