The paper refers the changes of Polish Higher Education, with special attention to the changes the autonomy and governance structures, in light of historical events and challenges for the future. For many decades, the Polish system of Higher Education remained unchanged, basing on the structure and mentality built on early 20th century foundations, petrified after 1945. The change of the political system in 1989 has not brought significant changes in the universities’ governance in science and education, although it has been relieved from the ideological supervision. Polish scientists appealed to change this more and more ineffective system mainly because of degrading organisational frames and governance structure. Polish universities dealt with crucial problems as the mismatch of the structure of the higher education system to social and economic challenges, limited financial autonomy of the university, unsatisfactory quality of higher education. The inbred nature of Polish universities and research and the system of scientific degrees and titles inhibits scientists’ pursuit of scientific excellence, interdisciplinary research, and, consequently – international recognition. In 2016 the Polish government started the process of the dialogue with the academic world in Poland, creating the foundations for the new, revolutionary bill of higher education called ‘The Constitution for Science’. The new policy of the Polish government bases, in theory, the transformation of universities on their internationalisation to make Polish science an equal partner for leading centres in the world. The new Act came into life in 2018, but its implementation at Universities generally started in October 2020. The paper describes the foundations of the changes and demonstrates the implementation process on the example of leading universities in Poland. The example of changes in Polish education can serve as a source of reflection on the impact of political changes and European Union support on the process of democratization of university structures and on how this process affects the quality and freedom of research and education in countries behind the former Iron Curtain.