As the worldwide economic paradigm changes, higher education becomes an extremely important factor in ensuring a country’s scientific and technological sovereignty. This article compares the state of higher education in the Russian Federation (RF), the Republic of India (RI), and the People’s Republic of China (PRC) and ranks the development of their respective higher education systems in order to derive a model for advancing the innovative competitiveness of the RF’s institutions of higher education and to identify the components required to make them more competitive. Study of statistical data and regulations along with retrospective and systemic structural analysis indicate that program and process management is an innovative way to increase the competitiveness of universities. This result is grounded in a descriptive analysis of previous scientific studies, which substantiated the authors’ definition of what makes universities competitive. Comparison of the programs and projects implemented in the three countries examined leads to the conclusion that the RF should accelerate the creation of a wide network of program and project initiatives in higher education. Although a comparative analysis of the RF’s nationwide Project 5–100 and Priority 2030 program reveals certain problems in university management, it also establishes that applying existing regulations for strategic planning as well as for program project management in order to develop universities can assist in reaching the targets of Presidential Decree No. 145 dated 28 February 2024, entitled “Strategy for Scientific and Technological Development of the RF” (SSTD).