The article reveals issues of building the innovative ecosystem institutions problem in context of the growing role of research Universities in ensuring innovative structural changes in the economy of Ukraine. International comparisons of the actual state of effectiveness and development potential of Ukraine’s innovation ecosystem have shown that it lags behind almost all indicators of the European Innovation Scoreboard. It is a confirmed necessity to form in Ukraine a state innovation policy based on criteria of the European Innovation Scoreboard with the goal of improving all its indicators, which comprehensively reflect the state of the national innovation ecosystem.It has been focused on the formation of the central link of the innovation ecosystem – the entrepreneurial innovation University as a progressive structural change’s generator in the economy. The justified urgency of increasing the state support for the priority development of research, design and development, and educational institutions that are part of national and regional innovation ecosystems. It is necessary to radically increase the volume and change structure of the state funding of institutions in the field of research and development, as well as innovation activity, reducing the share of the state funding of individual projects and individual grants, which should be financed mainly by business structures.It is shown that the main practical problem in determining the place and role of research Universities and other scientific and educational institutions in the structural innovation transformation of the economy of Ukraine is insufficient attention to formation and implementation of the practical function of basic innovations as the main factor of economic growth. It is suggested under formation of the Ukrainian state innovation policy, a separate priority area related to the creation of higher education institutions (Universities) of new generation as innovative entrepreneurial Universities should be identified, while it is important to develop Universities and scientific centres that demonstrate the presence of cumulative human capital, despite their temporary state of crisis.
 JEL classіfіcatіon: I23, I25, L52, O38, P52