Research universities have emerged as a basic asset in international local institutions that contribute to the knowledge and socio-economic development of countries. Research universities in Turkey were established in national policies in 2017. This study aims to investigate the efficiency of ten research universities and five candidate research universities by the Council of Higher Education (CHE). The paper further aims at determining the factors that influence the efficiency of these universities on the basis of 2017 input and output data. As input variables, the number of faculty members per program and the number of scientific research projects were used in the efficiency analysis. As output variables, the ratio of the citation per publication in 2017 in Web of Science (WoS), the ratio of the research project income to the total appropriations, and the ratio of the PhD graduates to the number of PhD programs were used. Surprisingly, the number of scientific research projects in the major field of study negatively influences the efficiency scores of research universities. Instead of centralized management and output-oriented evaluation, university-based regulations must be identified, and process-oriented measures should be taken. The rate of citations per publication and the rate of PhD graduates per PhD program affect the efficacy scores positively. Because research as the main indicator of universities is well established, directing academics to scientific studies instead of course load is likely to increase the efficiency of research universities. Finally, focusing on doctoral education in terms of internationalization is likely to increase the scientific studies of universities and their quality development of research universities.