The Institute of Mathematics and Informatics takes part in the education of undergraduate and graduate students either as a partner in bilateral  cooperation agreements with other universities or through its experts: Sofia University – Faculty of Mathematics and Informatics, Plovdiv University, New Bulgarian University, South-West University in Blagoevgrad, University of Economics in Varna, University of Library Studies and Information Technologies, Technical University of Rouse, Higher School of Civil Engineering, American University in Bulgaria, University of Telecommunications and Post in Sofia, University of Architecture, Civil Engineering and Geodesy, European Polytechnical University in Pernik, Burgas Free University, Veliko Tarnovo University,University of Finance, Business and Entrepreneurship in Sofia, Academy of Music, Dance and Fine Arts in Plovdiv, etc. IMI researchers are also visiting lecturers at foreign universities: Abdus Salam School of Mathematical Sciences in Pakistan, AwesomeMath, University of Santa Cruz and Cornell University in USA, Université des Antilles, University of Ljubljana in Slovenia, Software Institute of the Chinese Academy of Science, etc.

IMI and the New Bulgarian University have a bilateral cooperation agreement under which the two institutions offer three joint Master degree programs: Applied Statistics, IT Project Management and Financial and Accounting Management and Insurance.

Since 2012 IMI and the Faculty of Mathematics and Informatics of Sofia University have signed a cooperation agreement for internship programs im mathematics and computer science. In 2013 IMI took part as an employer in the Student Internship Project of the Bulgarian Ministry of Education and Science, offering over 30 topics in mathematics and computer science. In the period from August till December 2013, over 10 undergrad students from several universities underwent 240-hour practical training under the supervision of researchers from IMI.