The execution of the policies laid down by the Board of Trustees is the responsibility of the Board of Governors. The Rector of the university is the Chairman of the Board of Governors. The Board of Governors consists of the following members:
Rector, IIU (Chairman)
  Prof. Dr. Samina Malik
President, IIU (Vice-Chairman)
  Prof. Dr. Hathal Hamoud Alotaibi
Chief Justice, Federal Shariat Court, Islamabad or his nominee
  Hon. Mr. Justice Iqbal Hameed Ur Rahman,
Chief Justice, Federal Shariat Court of Pakistan, Islamabad
Secretary, Ministry of Education (Member)
  Mr. Waseem Ajmal Chaudhary,
Federal Secretary, Ministry of Federal Education and Professional Training, Islamabad
Chairman, HEC or his nominee (Member)
  Prof. Dr. Mukhtar Ahmed
Chairman, HEC
One Vice-Chancellor of a Pakistani University to be nominated by the Chancellor (Member)
Three nominees of the Pro-Chancellor (Members)
  Prof. Dr. Naseer Ahmed Akhtar,
Dean, Faculty of Social Sciences & Chairman, Department of Islamic Studies,
The University of Lahore

Dr. Muhammad Aamir (Tuaseen),
Chief Executive Director,
Majilis Ilmi Foundation, Karachi, Pakistan

Maulana Saeed Yousaf,
Jamia Dar-ul-Uloom Taleem-ul-Quran,
Plandari, Azad Kashmir, Pakistan

Three nominees of the Board of Trustees (Members)
Secretary Board of Governors