Background We retrospectively analyzed risk factors for late bronchopleural fistula after non-small cell lung cancer (NSCLC) surgery and compared with those for early bronchopleural fistula. Methods In all, 6,239 patients with NSCLC who underwent surgery were studied, and clinical risk factors were examined by univariate and multivariate analysis. This study included 23 patients (0.38%) with late bronchopleural fistula and 43 patients (0.65%) with early bronchopleural fistula among all 6,239 patients. Follow-up data were recorded until December 2005 or until death. Statistical significance was calculated using the log rank test. Results By univariate analysis, patients with radiotherapy after operation, pneumonia after operation, pneumonectomy, and advanced age were related to higher risk of bronchopleural fistula. In the multiple logistic regression models, both pneumonia and operative procedure were among the independent risk factors of early and late bronchopleural fistula. Early bronchopleural fistula was observed primarily in the aged. Late bronchopleural fistula was associated with postoperative radiotherapy. The average intervals of bronchopleural fistula between pneumonectomy and lobectomy were significantly different. Compared with the mortality rate of late bronchopleural fistula (0%), the mortality rate of early bronchopleural fistula (11.6%) was significantly higher. Conclusions There are both similarities and differences between the risk factors for early and late bronchopleural fistula. We should analyze the different reasons for the occurrence of bronchopleural fistula, and adopt different preventive measures. Different follow-up should be provided for the different operations.