Higher education is a public good as well as a public responsibility. It is realized from higher education institutions and is regulated by higher education legislation in the Republic of Albania. From January 2014 in Albania started a reform process in higher education and research. The way how this reform is realized is a particular way because the drafting of it is entrusted to an independent Commission. The Commission consists of academics and experts in higher education. The result of the reform consists in a draft law which abrogates the law no.9741, dated 21.5.2007 “On higher education in the Republic of Albania”. The draft law has already initiated its legislative process. This paper seeks to be one of the first works that examines some of the innovations in this draft law. The draft consists of thirteen chapters. In my opinion two are the most important innovations. The first innovation relates to the proposal of a new way of organizing and functioning of institutions of higher education which clearly separates academic and administrative leadership. The highest academic governing body is the Academic Senate and the highest academic authority remains the Rector of the Institution which is its legal representative for academic affairs. The highest administrative governing body is the Board of Administration, which guarantees the fulfilment of the mission of the institution and its financial and administrative conduct. The draft law creates a new figure who is the administrator of the Institution who is the highest administrative authority responsible for the financial functioning of the institution. The administrator is the legal representative of the institution for financial and administrative matters. This paper will analyze the relationship between academic and administrative structures. A hotly debated innovation of the reform is the creation of another type of institution which is the Independent public institution of higher education known as a public legal person. The special thing about this institution is that it is created as a result of the transformation of the existing institutions of higher education, on their demand, but only when they meet preset criteria set by law. Can be transformed into public legal persons not only public institutions, but also non-public higher education. The new institution is non-profit and regardless of the origin of the foundation, the institution applies the same rules of organization. To the new institution will apply the provisions for public institutions of higher education in all cases when is not otherwise provided. The methodology used will be analytical. DOI: 10.5901/ajis.2015.v4n2s2p46