The proper development of transportation constitutes the basis for an effectively functioning economy at the national and global levels. On the other hand, transportation significantly impacts the environment and climate. Sustainable transportation management should therefore include both economic, social and environmental aspects. The article aims to comprehensively assess the economic–energy–environmental efficiency of the 27-road freight transport sector in EU countries in 2019. The research was conducted using the non-parametric Data Envelopment Analysis (DEA) method. The Slacks-Based Measure–Data Envelopment Analysis (SBM-DEA) model was used, taking into account unwanted (undesirable) effects. As non-energy inputs in the DEA model used the labor in the road freight transport sector, stock of registered goods vehicles, and the length of the road network. Moreover, the energy consumption by the road freight transport sector was used as energy inputs in the DEA model. Desirable outputs were taken as road freight transport sector revenues and freight work performed by the sector. GHG emissions expressed in CO2 equivalent were treated as undesirable outputs. The research also adopts energy productivity and GHG emission efficiency indicators. The eco-efficiency of the road freight transport sector in EU countries varies. Ten countries have efficient road freight transport sectors. The efficient road freight transport group included Denmark, Germany, Belgium, Lithuania, Luxembourg, the Netherlands, Poland, Portugal, Slovenia and Bulgaria. They efficiently transformed the inputs into outputs. Five countries were recognized as eco-efficiency followers, including Italy, Finland, Slovakia, Sweden and Romania, and 12 countries were characterized by an inefficient road freight transport sector. Based on benchmarking principles for inefficient road freight transport sectors, the changes in input and output levels were proposed to improve efficiency. The relationship between the economic development of EU countries and the eco-efficiency of the road freight transport sector was also analyzed, indicating a positive relationship between the variables but with weak strength. The main contributions of this article are an extension of previous DEA works that assesses the efficiency of the road freight transport sector, also considering undesirable variables. Research conclusions are particularly important for policymakers in the context of management sustainable transportation development in the EU.