The articles purpose is to examine the effectiveness of the higher education reforms in Uganda and assesses the fit of the organisation structures of the University and Other Tertiary Institutions Act of 2001 to the higher education strategy of the Ugandan government. The study is the first analytical case study of higher education reforms in Uganda from the contingency theory's perspective of a fit among the business environment, organisation structure and strategy the findings indicate the functional organisation structure imposed on the public universities and tertiary institutions are inappropriate but the legislation needs to be amended to address some shortcomings in its design. As parliamentary action is needed the amendments are likely to be controversial. The study may lead to changes in the legislation and improve the effectiveness of university administration in Uganda and provide some insight for other developing countries in the process of reforming their higher education sectors