The preparations for the establishment of the University of Eastern Finland began in 2006. In October 2006, the Ministry of Education chose the collaboration model between the University of Joensuu and the University of Kuopio as one of the national-level spearhead projects in structural development. Led by Professor Reijo Vihko, the report of the working group preparing the project was completed in February 2007. The objective of the project was to establish the University of Eastern Finland, which was to be a federal university in terms of its administrative structure. Originally, the collaboration between the University of Joensuu and the University of Kuopio was rooted in their aspirations to obtain a shared right to confer degrees in economics and business administration, but already in the report of Vihko’s working group, the collaboration was extended to natural sciences and social sciences. However, the federal university was never formed, as the preparations for a full merger of the universities and their activities was launched in autumn 2007. In spring 2008, the University Senates of both universities approved the merger and the scientific and administrative structures the new university was to have. In 2009, a strategy and administrative regulations were prepared for the University of Eastern Finland, and the contents of the degree programmes were decided upon. The right to confer degrees in economics and business administration was obtained at the time of the merger, in 2010. In other words, the University of Eastern Finland was built on a tight schedule and it began operations in the beginning of 2010.
The University of Joensuu was established in 1969. In Finnish, it was first known as Joensuun korkeakoulu and, since 1984, as Joensuun yliopisto. In the beginning, the main focus of the university was on teacher education. Forest sciences was the first field of study not linked to teacher education that began to be taught in Joensuu after a long and colourful debate in 1982. In addition to forest sciences, the launch of education in theology was also a topic that inspired plenty of discussion. The degree programme in Orthodox Theology began in 1988. Western Theology became available for subject teachers in 1997, and education in Western Theology leading to positions within the church began in 2001. Before the merger of the University of Joensuu and the University of Kuopio, Bachelor's, Master's and doctoral level education was offered at the University of Joensuu in eight fields of study.
The University of Kuopio was established in 1972, offering education in medicine, medical physics and biochemistry. The year 1973 witnessed the launch of education in pharmacy, dentistry and environmental hygiene. The University of Kuopio, too, was first known in Finnish as Kuopion korkeakoulu and, since 1984, as Kuopion yliopisto. In 1984, the university began offering education in social work and clinical nutrition. In 2002, the University of Kuopio was the largest provider of medical education in Finland. Before the merger, the University of Kuopio had five faculties.