This paper explores the structural and operational dimensions of the efficiencies of airports. The two-stage procedure is suggested to assess the efficiencies of airports in this study. In the first-stage, Classification and Regression Tree, which is one of the machine-learning approaches used to divide the airports into homogeneous and thus comparable sub-groups. In the second stage, the bootstrap data envelopment analysis approach obtains more precise structural and operational efficiency scores. To illustrate the proposed framework use, we applied it to a real case associated with Turkish airports. The results demonstrate that this framework presents a more comprehensive assessment of airport performance rather than conventional data envelopment analysis models. Moreover, it provides to show the deficiencies of the structural and operational management of airports. The findings can help anywhere airport authorities as well as Turkish airport authorities.