Like other transitional countries, the Western Balkans face educational challenges due to the long transition period, respectively centralised educational activities associated with a dearth of scientific activities, and limited academic freedom. The previous centralised political and economic system in the Western Balkans created the academic community's dependence on the political system in some of these new countries. Kosovo is a point in the case. The purpose of this study is to address some aspects which have an impact on academic freedom within higher education institutions (HEIs) in Kosovo: (1) freedom to research and teach; (2) freedom of academic exchange and dissemination; (3) institutional autonomy; (4) campus integrity; and (5) freedom of academic and cultural expression. To analyse universities' challenges concerning academic freedom, we conducted a survey with academic staff at the largest public university in Kosovo, the University of Prishtina. This study is the first attempt to construct and analyse the academic freedom, providing a framework for analysis and debate of academic freedom in Kosovo. The results show that compared to previous decades (1981-1999), there is improved academic freedom in Kosovo. However, considering the latest developments and opportunities coming from the European Union (EU) programs and cooperation with EU universities, there is still a possibility of further advancing academic freedom within HEI, focusing on supporting academic integrity, institutional sustainability, and cooperation.