Alex Ekwueme Federal University, Ndufu-Alike (AE-FUNAI) runs its academic programmes through the faculty and collegiate system. Each faculty/college houses various departments.

• Faculty of Agriculture

• Faculty of Basic Medical Sciences

• Faculty of Education

• Faculty of Engineering and Technology

• Faculty of Environmental Sciences

• Faculty of Humanities

• Faculty of Law

• Faculty of Management Sciences

• Faculty of Biological Sciences

• Faculty of Physical Sciences

• Faculty of Social Sciences

• College of Medical Sciences