In 1971 the Institute for Development of Mathematics Education (IOWO) was established at Utrecht University, with the mathematician Prof. Dr. Hans Freudenthal as its professor-director. This institute was a formalization of the work of the Committee on the Modernization of the Mathematics Curriculum (CMLW), who had, in the sixties, the task to make mathematics education in primary and secondary schools better prepared for further education. The activities of the institute concentrated on the projects Wiskobas, mathematics in elementary school, and Wiskivon, mathematics in secondary school. The IOWO worked on the development of mathematics education in cooperation with schools were the curricula were tested. During this time, the so-called Realistic Mathematics Education (RME) emerged, an approach that became quite popular.
In 1981 the IOWO was disbanded as a result of budget cuts and a redistribution of tasks. In the form of the department of Research in Mathematics Education and Education Computer Center (OW&OC), led by Prof. Dr. Frederik van der Blij, a much slimmed down group was able to continue the work of the IOWO. The OW&OC was given a role (among others) in the development of the new curricula for Mathematics A (after the redistribution of Mathematics 1 and 2). After the death of Hans Freudenthal in 1990, the now grown OW&OC was renamed the Freudenthal Institute in 1991. The group was increasingly concerned with design research, a method in which the development of teaching materials and subject matter research go hand in hand. Much attention was paid to the use of digital technology in mathematics education, as evidenced by the development of the Digital Mathematics Environment.
After already being formally part of the science didactics groups under the name CD-b since 1989, the Freudenthal Institute officially merged with the science didactics groups under the name Freudenthal Institute for science and mathematics education (FIsme) in 2006. However, the two groups still remained physically separated until the mathematics group also moved into the Buys Ballot Building in 2010. In 2014, the merger with the History and Philosophy of Science department took place, from which the current Freudenthal Institute emerged.