As a postdoctoral researcher at the Max Planck Institute for Biological Cybernetics, he carried out research on the structure of the cerebellum for four years. Together with the theoretical physicist Tomaso Poggio, Manfred Fahle received the Max Planck Research Award for work stemming from his time at the Massachusetts Institute of Technology. From 1999 onwards, Manfred Fahle worked at the University of Bremen. Here, he was the managing director of the Center for Cognitive Sciences (ZKW), professor of human biology, chairman of the Research Committee, and a member of the Academic Senate.