The Max Planck Institute for the History of Science comprises three departments under the direction of Jürgen Renn (I), Etienne Benson (II), and Dagmar Schäfer (III). In addition are Research Groups, each directed by one junior Research Group Leader or Coordinator.

The Institute also comprises of a Research IT Group—specialist in digital humanities—and International Max Planck Research School (IMPRS), doctoral students, and research and teaching cooperations with other institutions worldwide.