Pakistan and the Czech Republic have a mutually beneficial cooperation in the field of education. According to the Czech National Agency for International Education & Research, approximately 390 Pakistani students are studying in the Czech Republic in 2023. Most of these students are enrolled at Charles University, followed by Czech University of Life Sciences Prague and Masaryk University. The remaining students are primarily studying at various other public sector universities, evenly distributed amongst various disciplines e.g. medicine, engineering, ICT, business studies etc. Pakistani students also come to the Czech Republic under the Erasmus program, for shorter term. The Czech Ministry of Foreign Affairs has a dedicated department dealing with the international cooperation between universities.

The Mission has also been directly engaged with major public/private sector universities in the Czech Republic. A number of meetings between the Ambassador, Rectors/Vice Deans of respective universities in Pakistan and the Czech Republic have been held and they have shown keen interest in visiting Pakistan and exploring cooperation with Pakistani universities for joint research, student/faculty exchange and joint supervision of projects. A number of MoUs are under consideration in this regard.