The research aims to study the role of contemporary universities in developing education on green economy and sustainable development in the Kyrgyz Republic. To achieve the research goal, the authors applied the methods and principles of social cognition and comparative-logical analysis of socio-humanitarian literature. The research object is the higher education system of the Kyrgyz Republic and educational institutions of higher education as elements of this system. As a result of the research, the authors found that universities in Kyrgyzstan mostly realize their main functions through supporting national priorities of higher education in the green economy and sustainable development. Additionally, the authors identified the problems that objectively restrain the process of introducing the principles of green economy in higher education institutions of Kyrgyzstan. The prospects for developing the University 4.0 model in the context of the green economy are outlined. According to the analysis results, the authors concluded that the actualization of the universities’ role in training human resources for green economy implies ensuring global competition of educational programs and graduates in the field of sustainable development and green economy in the national and international labor markets. The obtained results make it possible to comprehend the innovative role of contemporary universities in a new way as a new paradigm of the development of a green economy and green transformation of the higher education system.