South Eastern Kenya University has 8 schools. The University has enrollments for undergraduate, graduate, diplomas, certificate and professional students.
- School of Agriculture and Veterinary Science
- School of Business and Economics
- School of Education,Humanities and Social Sciences
- School of Pure and Applied Sciences
- School of Environment, Water and Natural Resources Management
- School of Engineering and Technology
- School of Information & Communication Technology
- School of Nursing Sciences and Public Health