The University of Tartu improved its position as Tallinn University of Technology featured for the first time on the top 500 list in this year's QS World University Rankings.
The University of Technology claimed a place between 441-450, becoming the highest ranking university in Estonia and the Baltics.
On the list, which was published on Tuesday, University of Tartu rose from the group ranked 501-550 to 461-470.
Tallinn University of Technology ranked high (158th place) in the faculty to student category, but fell in the citations per faculty category (652), while Tartu also excelled in the faculty to student category (313), but fell in the international students category (666).
Estonia's third big college, Tallinn University, did not make the list.
The Massachusetts Institute of Technology (MIT), Harvard University and the University of Cambridge topped the list, while the University of Latvia, along with three Lithuanian universities was placed in the 701+ group, and Vilnius University placed 601-650.
Nine Finnish universities made the list, with the University of Helsinki the highest, at 69. Russia's highest entry is the Lomonosov Moscow State University, placed 120th.
The QS World University Ranking is one of three major ranking lists for higher education facilities. The Academic Ranking of World Universities features no university from Estonia on its top 500 list, while the Times Higher Education Ranking places Tartu as the only Estonian entry, in the 351-400 group.