The mirror of a country’s scientific identity and strength is its universities. The greater the concentration of universities that stand out in terms of scientific publication performance, approved project performance, and the quality and performance of academic staff, the more diverse and powerful the country’s scientific ecosystem becomes. This strength has positive economic, social, and moral impacts on society. Research universities, which constitute a class formed according to the scientific identity of universities and aim to make a difference in technological development, have the most crucial role in ensuring this impact. International and national rankings based on universities’ academic performance criteria not only contribute to universities’ future planning but also influence the approaches of governments and international organizations toward universities. The subject of this study is to reveal the performance of research universities in Türkiye within the scope of the University Ranking by Academic Performance (URAP) and the TÜBİTAK Entrepreneurial and Innovative University (EIU) Index. The study aims to compare the performance rankings of research universities in Türkiye according to the URAP and EIU indices. Within the framework of the research question of whether there is a statistically significant relationship between research universities and the URAP and EIU index rankings, the literature on the concepts of research universities, URAP—which is an international academic performance-based university ranking—and the EIU Index, which includes TÜBİTAK’s evaluation criteria for universities, was examined. Open-access internet resources such as books, journals, and articles were reviewed through document analysis within the scope of qualitative research methods and analyzed using a systematic analysis approach. In addition, analyses were conducted using the SPSS 25 (Statistical Package for the Social Sciences) software to determine whether there is a significant relationship among the 2025 research universities ranking, the rankings of research universities in the 2025–2026 URAP general university ranking, and the rankings of research universities in the TÜBİTAK 2024 EIU Index. As a result, there is a positive, significant, and strong relationship between the 2025 research university rankings and the 2024 TÜBİTAK entrepreneurial and innovative university index rankings; there is a positive, significant, and moderate relationship between the 2025 research university rankings and the 2025-2026 URAP rankings; A positive and significant relationship was found between the 2024 TÜBİTAK entrepreneurial and innovative university index ranking and the 2025-2026 URAP ranking.