EAIFR has two levels of governance. The first is the Steering Committee which is made up of representatives of the Rwanda Ministry of Education, the ICTP, the University of Rwanda and other stakeholders. The Steering Committee sets general guidelines for the institute's activities, determines budgeting levels, and considers proposals from the Director for the programme, work plans, financial plans, and budget.

The second is the Scientific Council which is composed of distinguished scientists in the areas of interest to the institute. This council advises EAIFR on its programmes of activities, taking into consideration major academic, scientific, educational and cultural trends relevant to the institutes' objectives.

EAIFR Steering Committee:

• Mike Hughes, Adviser, Science and Technology,Rwanda Ministry of Education (Steering Committee Chair)
• Omololu Akin-Ojo, Director, ICTP-EAIFR (ex-officio)
• Nosa Egiebor, Professor and Deputy Vice Chancellor, University of Rwanda
• Alan Mushi, Professor, University of Dar es Salaam
• George Thompson, Head, Office of Strategic Planning and Education, ICTP

EAIFR Scientific Council:

• Winston Wole Soboyejo, Worcester Polytechnic Institute (Chair of Council)
• Cynthia J. Ebinger, Tulane University
  
• George Ellis, University of Cape Town
• Ali Hassanali, ICTP
• Alik Ismael-Zadeh, Karlsruhe Institute of Technology
• Timoleon Crepin Kofane, University of Yaounde
• Shobhana Narasimhan, Jawaharlal Nehru Centre for Advanced Scientific Research
• Roy Maartens, University of the Western Cape
• Ravi Sheth, University of Pennsylvania
• Amanda Weltman, University of Cape Town