The Fraunhofer Institute for Systems and Innovation Research ISI closely cooperates with a large number of universities and with national and international partners and is a member in international network and advisory committees.

• Karlsruhe Institute of Technology (Chair Innovation and Technology Management at the Institute for Entrepreneurship, Technology Management and Innovation (ENTECHNON), Professor Marion Weissenberger-Eibl)
• Experts Dialogue of the Chancellor (head of the working group Innovation Culture, Professor Marion Weissenberger-Eibl)
  
• University of Hannover (Institute of Economic and Cultural Geography, Professor Knut Koschatzky)
• CEPE – Centre for Energy Policy and Economics at the Eidgenössische Technische Hochschule, Zurich (Prof. (em) Dr. Eberhard Jochem)
• Karlsruhe Institute of Technology (Chair of Energy Economics, Professor Martin Wietschel)
• University of Kassel (honorary professor for the energy sector, Professor Harald Bradke)
• Virginia Tech (Department of Agricultural and Applied Economics, Blacksburg (Prof. Dr. Joachim Schleich)
• TAB – Office of Technology Assessment at the German Parliament
• BETA  – Bureau d’Économie Theorique et Appliquée and LEA – Laboratoire Européen Associé at the Université de Strasbourg
• School of Public Policy of the Georgia Institute of Technology, Atlanta
• IPM – Institute of Policy and Management at the Chinese Academy of Sciences CAS, Beijing
• Eu-SPRI – European Forum for Studies of Policies for Research and Innovation
  
• DIME – Dynamics of Institutions and Markets in Europe
• ETEPS – European Techno-Economic Policy Support Network
  
• Six Countries Programme