The IIR has engaged in research of international relations for more than six decades. The IIR is a successor of the Institute of International Politics and Economics (IIPE), founded by the Ministry of Foreign Affairs in 1957. During the Prague Spring of 1968, the IIPE employees took an active role in the reform movement. As a result, it was dissolved in 1970, and the reform-minded researchers were laid off.

The same year the Institute was re-established as the Institute of International Relations (IIR) by the Ministry of Foreign Affairs. The relaxation of the latter part of the 1960s was over, and the Institute came under a strong ideological influence from the Communist regime for decades to come. Nevertheless, it continued to maintain its relations with colleagues abroad, including Western ones. The library played a significant role, as its funds got enriched by some foreign resources that were nowhere else to be found in then Czechoslovakia.

The fall of communism following the Velvet Revolution in 1989 meant radical personnel and organizational changes. With the influx of new employees, its research programmes and international connections were broadened and transformed substantially. The projects in which the researchers decided to participate expanded significantly, as the Institute launched a cooperation with similar foreign research institutions. An important role in steering the Institute in the new direction was played by Professor Otto Pick, its then director.

In the following years, the IIR expanded to include the Diplomatic Academy (which was incorporated in the Ministry of Foreign Affairs in 2007) and the Development Centre, which later turned into the independent Czech Development Agency (CDA). In addition to the theoretical quarterly International Relations, the Institute also began publishing the English language semi-annual journal Perspectives. The Institute also took over the popular monthly magazine Mezinárodní politika and brought it into its portfolio of periodicals.

The most recent era of its existence began in 2007, when the Institute was transformed into a public research institution in accordance with the Bill No. 341/2005 Coll., namely an institution which produces internationally competitive and socially relevant research of international relations and, in line with its mission, effectively broadens the horizons of the Czech debate about international politics.