The University of Zagreb, at the time the sole university in the People's/Socialist Republic of Croatia, was declaratively autonomous, although this was not possible in Yugoslavia, a state under communist rule. This paper thus explores the relationship between the University and the League of Communists of Croatia from 1959 to 1965, as well as the modes whereby the League of Communists influenced the University's work and organization in terms of self-management socialism. The study is based mostly on previously unexplored archival records and the relevant literature. The results show that Marxist ideology continued to be the foundation of power, and the University continued to implement the guidelines of the League of Communists, even though the new direction of self-management socialism had been introduced. The entanglement between the League of Communists and state functions with University authorities was evident, and one of the essential features of the regime. However, the communists confronted insufficient support for their activities from most of the professors and a portion of the student body.