The Freudenthal Institute offers two Master's programmes:
- A two-year research master's History and Philosophy of Science, in cooperation with the Descartes Centre for the History and Philosophy of the Sciences and the Humanities. This master's degree is part of the Graduate School of Natural Sciences.
- A two-year master's Science Education and Communication. This master's degree is part of the Graduate School of Teaching. The Freudenthal Institute offers two profiles for students who do not do the Master's in Science Education and Communication, but do have an interest in education and communication.
In addition to these two Master's programmes, the Freudenthal Institute, together with the Graduate School of Teaching, also offers one-year teacher training courses for all science school subjects.