Background Community-acquired pneumonia is one of the most common infectious diseases in children and is a leading cause of death among children under 5 years of age, resulting in high rates of antibiotic usage and hospitalization. It is of extremely practical significance to make full use of the existing electronic medical records to study pneumonia and to establish automatic diagnosis models for pneumonia. Methods We established pneumonia diagnosis models of Bayesian network using a total of 13,448 electronic medical records. We investigated learning network structure and parameter estimation and evaluated different structure learning strategies and various modeling methods. By identifying the key predictors of model, the pneumonia status was analyzed. Results The performance of the proposed Bayesian network was evaluated using a set of 3361 cases with a precision of 0.7861, a recall of 0.9889, and an F1-score of 0.8759. On an independent external validation set containing 4925 cases, Bayesian network achieved a precision of 0.7382, a recall of 0.9947, and an F1-score of 0.8475. Our proposed Bayesian network outperformed all other methods, including CatBoost, XGBoost, LightGBM, logistic regression, and ridge classification. Conclusion The appropriate feature selection improved the performance of Bayesian networks. The proposed Bayesian network had good generalizability and could be directly applied to clinical research centers. And the key predictors identified by the network demonstrated good clinical interpretability, allowing for a better understanding of pneumonia status and complications. This study had important clinical value and practical significance for the research and diagnosis of pediatric pneumonia.