The Office of the Vice-Chancellor is headed by a Vice-Chancellor who is the Chief Executive Officer of the University and is appointed by the Cabinet Secretary, Ministry of Education, Science and Technology in consultation with the University Council.

The Vice-Chancellor is answerable to the Egerton University Council for the overall management of the University, and is the Chair of the University Management Board and the Senate.

Prof. Isaac O. Kibwage, HSC is the Vice-Chancellor of Egerton University, where he directs the institution's strategic planning, policy execution, and overall governance. A distinguished Professor of Pharmaceutical Chemistry on leave from the University of Nairobi, he brings decades of top-tier academic, financial, and administrative leadership.

He previously served for a decade as the Principal of the College of Health Sciences at the University of Nairobi, transforming it into an EAC-recognized "Center of Excellence" and quadrupling its research funding. A Fellow and former 6-year Chairman of the Pharmaceutical Society of Kenya, his exemplary services to healthcare and higher education earned him the prestigious Head of State Commendation (HSC).