Objective To analyze the therapeutic effect of fiberoptic bronchoscopy alveolar lavage in the treatment of children with pneumonia and atelectasis. Methods: 160 children with pneumonia complicated with atelectasis admitted to our hospital from October 2022 to February 2025 were selected as the research subjects. The children were randomly divided into the control group and the study group, with 80 cases in each group. The control group was given conventional treatment. The research group performed fiberoptic bronchoscopy alveolar lavage. The therapeutic effects, improvement time of clinical symptoms, pulmonary function [forced expiratory volume in one second (FEV1), forced vital capacity (FVC)], blood gas indicators [arterial oxygen saturation (SaO2), arterial partial pressure of oxygen (PaO2), arterial partial pressure of carbon dioxide (PaCO2)], inflammatory factors [interleukin-6 (IL-6), primordial hormone (PCT), hypersensitive C-reactive protein (hs-CRP)], and the occurrence of complications of the two groups were analyzed and compared. Results: The total effective rate of treatment in the study group was significantly higher than that in the control group (P < 0.05). The disappearance time of clinical symptoms such as cough, fever, shortness of breath and rales in the study group was significantly shorter than that in the control group (P < 0.05). After treatment, the levels of FEV1 and significant FVC in both groups were significantly higher than those before treatment, and the levels of FEV1 and FVC in the study group after treatment were significantly higher than those in the control group (P < 0.05). After treatment, the levels of SaO2 and PaO2 in both groups were significantly increased compared with those before treatment, while the level of PaCO2 was significantly decreased. Moreover, the levels of SaO2 and PaO2 in the study group after treatment were significantly higher than those in the control group, and PaCO2 was significantly lower than that in the control group (P < 0.05). After treatment, the levels of IL-6, PCT and hs-CRP in both groups were significantly lower than those before treatment, and the levels of IL-6, PCT and hs-CRP in the study group after treatment were significantly lower than those in the control group (P < 0.05). The incidence of complications in the study group was significantly lower than that in the control group (P < 0.05). Conclusion: Fiberoptic bronchoscopy alveolar lavage for children with pneumonia and atelectasis can improve the therapeutic effect, promote symptom resolution, improve lung function and blood gas indicators, reduce inflammation, and decrease complications.