The University of Malawi is the oldest and, arguably, the most prestigious university in Malawi. It was established immediately after the country became independent and has gone on to train a multitude of prominent Malawians in various disciplines. This article’s focus is on academic freedom and institutional autonomy in this University, especially in the period after 1994 when Malawi made the transition from a dictatorship to a multiparty democracy. This article adopts the position that institutional autonomy is necessary for a university to function properly, but that it remains seriously compromised in the University of Malawi. To illustrate this argument, the article focuses on the following: the manner in which the university has managed its undergraduate admission policy; the government’s approach to funding the University; the University’s management of disputes pertaining to increments in students’ financial contributions; the University’s handling of disputes in relation to academic freedom; and also the position of the President as the Chancellor of the University. In all the aforementioned areas, the article establishes that the practice in Malawi has routinely emasculated the lawful decision makers within the University thereby creating space for political leaders to either unduly influence decisions of, or actually make decisions for, the University which in turn compromises academic freedom and denudes the University of its autonomy.