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The purpose of the article was to study the processes of state regulation of the higher education system in Ukraine in the context of ensuring the autonomy of universities. General and special scientific methods were used in the research process. It was determined that the target priorities of the regulation of higher education system development are: a) regulatory influences on higher education institutions; b) promotion of the level of investment attractiveness of the higher education system; c) optimization of the use of limited financial resourcesn and; d) improvement of approaches to distribution of state orders for personnel training for the national economy, which further includes: state financing of research works carried out by higher education institutions. In conclusion, it has been proved that in order to ensure modernization changes in the higher education system, it is necessary to stimulate enterprises to cooperate with universities in the spheres of education and scientific research; to stimulate the inflow of investment resources from the business sector into the higher education system and to improve specific financial support tools for higher education institutions and enterprises developing cooperation with universities.