The main governing bodies of the University of Prishtina are the Governing Council and the Senate. The Governing Council has overall strategic responsibility for the effective institutional functioning of the university.

The Senate is the highest academic body of the university. It is headed by the rector of the university, who is the main managing authority of the university. The rector is the main academic and administrative leader and is responsible for the effective and regular work of the university and for its management according to the policy determined by the Governing Council. The rector is assisted by the vice-rectors and the general secretary of the university. The duties of vice-rectors are assigned by the rector, following the provisions of the UP Statute.

The general secretary of the university is the highest executive and administrative officer of the university. He answers to the rector for efficient, economical, and effective administration at all levels of the university.