Aim. To study new challenges and priority tasks facing universities within the framework of the new priority of the state scientific policy of Azerbaijan, as well as to identify problems related to scientific activity in universities of the republic in the context of world experience, and to make proposals on issues related to their solution.Tasks. To determine approaches and priorities for ensuring the effectiveness of scientific and pedagogical activity in modern universities, opportunities to develop new strategies of activity.Methods. In developing the conceptual provisions of the study within the framework of dialectical and systemic approaches used such methods of general scientific knowledge as historical and logical, abstraction, analysis, synthesis, the unity of objective and subjective in the development of economic processes. Economic and statistical, factor, functional and comparative methods of analysis were widely used. The methodological basis of the study also served as a systematic approach to the disclosure of institutional development of the state science policy of Azerbaijan. The author applied methods of scientific analysis, in particular, statistical; methods of comparative, fundamental and functional analysis. The article reflects the ideas stated in the scientific works of scientists-economists devoted to the problems of institutional development of the state science policy of Azerbaijan.Results. The triad “education — science — innovation” in universities forms the basis of their activity. Therefore, there is a need to rid scientific activity from its formal character and abstract content, as well as to change the traditional approach to the management of scientific activity in universities. Recommendations and proposals for improving educational-research-innovation efficiency in higher education in accordance with the requirements of the modern period, adequate to the peculiarities of the national economy development, have been developed.Conclusions. It is expected that by 2030 Azerbaijan will become an economically more developed and competitive country. Achievement of this goal depends on the presence of national scientific-innovative universities that ensure the use, assimilation and dissemination of new knowledge and technologies in Azerbaijan.