In the global QS World University Rankings, Masaryk University is ranked 454^th out of 1,504 institutions in 2026. Among Czech universities, Masaryk University takes 3^rd place behind the leading Charles University and the second Czech Technical University. This year's achievement is an improvement of 25 places in the Academic Reputation indicator to 358^th position and of 59 places in the International Research Network indicator to 296^th position in the global comparison . Among the Top 300 best institutions, MU was also ranked in the International Students indikator at 257^th position and the Sustainability indicator at 263^th position.

The QS rankings gives great importance to the area of research and development, which accounts for 50% of the overall ranking. In this area, it tracks both the institution's reputation among academics worldwide (through a separate QS survey) and the proportion of citations per academic and R&D staff member at the institution. The reputation survey may in particular counterbalance cultural differences, and peer review also gives humanities-oriented universities a chance to be ranked.