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Over the last two decades, application of Data envelopment analysis (DEA) in transportation problems have gained considerable research attention. This paper presents a literature review and classification of the applications of DEA in transportation systems (TSs). First by classifying 40 papers from 2007 to 2018, the origins of DEA in transportation problems have been reviewed. Then the development and an overall view of DEA applications in TSs have been presented. We have classified the applications of DEA into six different contexts. In each context, published papers have deeply been analyzed. Content of analysis includes "Number of published papers during the time", "target journals", "countries", "keyword frequency", "most cited papers", "map of most co-cited publications". More important, we reported the "inputs and outputs variables" used in each paper. Further "a review of the selected papers" and "gaps / future research directions" have been given within each cluster. The results show that DEA is one of the most useful approach in evaluating TSs for policy makers. On the other hand, DEA can help the decision makers in transportation especially regarding environmental factors, sustainable development and eco-design. Finally, we proposed subjects for future researches including guidance for new studies in the field of DEA applications in TSs.