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.

ICTP-EAIFR Steering Committee includes:

• Mike Hughes, MINEDUC Representative, Steering Committee Chair
• Dr. Amal Kasry, UNESCO Representative, Steering Committee Member
• Dr. Raymond Ndikumana, University of Rwanda (UR), UR VC Representative, Steering Committee Member
  
• Professor Alan Mushi,  University of Dar es Salaam, IUCEA Representative, Steering Committee Member
• Dr. Ali Hassanali, Senior Scientist, ICTP
• Professor Wole Soboyejo, Chair, ICTP-EAIFR Scientific Council (Invited ex-officio)
• Director of ICTP-EAIFR, Invited ex-officio

EAIFR Scientific Council includes:

• Professor Winston Wole Soboyejo, Worcester Polytechnic Institute (Chair of the Scientific Council)
• Professor Cynthia J. Ebinger, Tulane University
  
• Professor George Ellis, University of Cape Town
• Dr. Abdelkrim Aoudia, Senior Scientist, ICTP
• Professor Alik Ismael-Zadeh, Karlsruhe Institute of Technology
• Professor Shobhana Narasimhan, Jawaharlal Nehru Centre for Advanced Scientific Research
• Professor Ravi Sheth, University of Pennsylvania
• Professor Amanda Weltman, University of Cape Town
• Director of ICTP-EAIFR