The ranking of national universities provides an additional means of gauging the performance of universities that have not yet been included in global rankings. In the case of Madagascar, we proposed the implementation of a multi-criteria decision support system, designated as MadUrank, for the purpose of ranking the six public universities in the country. The system employs two distinct methodologies. Firstly, the method based on the removal effects of criteria (MEREC), is used to establish the relative importance of the criteria. Secondly, the combined compromise for ideal solution (CoCoFISo) method, is employed to determine the ranking of universities. The selection of criteria was based on the availability of data, with five criteria ultimately chosen. These were the number of students registered (STUREG), the ratio of students to administrative and technical staff (ATS), the ratio of students to permanent teachers (PTEACH), the success rate in examinations (SUCCES), and the percentage of students receiving scholarships (STUSCHO). The data set comprises observations from 2016 to 2020. In consideration of the data set, the MEREC method afforded priority to the STUREG criterion for the years 2016, 2017, and 2020, and to the STUSCHO criterion for the years 2018 and 2019. In accordance with the aforementioned priority criteria and the data set, the CoCoFISo method designated the Université d'Antananarivo as the top-ranked institution in 2016 and the Université de Fianarantsoa as the top-ranked institution from 2017 to 2020.