University autonomy is a principle recognized in the Constitution, however, there are violations that violate its freedom of leadership among its authorities, by attending to alternatives and gender equity, in accordance with the law. Over the years, the universities have struggled against the interventions suffered due to cuts in economic resources. Although they have worked with their own resources to sustain and cover themselves from attacks and attempts at direct intervention, their impact on professional and scientific development has been aggravated. For this reason, the present study is required to carry out an analysis of the factors that have the greatest impact on university autonomy and to determine possible solutions, which have transcended in the history and debate of Peruvian universities. For the modeling, the AHP methods of Saaty and TOPSIS were implemented with results to initiate the creation of mechanisms that contribute to the achievement of university, financial, academic and administrative autonomy.