| Master of Business Administration (MBA) |
| Master of Arts in Economics |
| M.Sc. Hospitality and Tourism Management |
| Master of Science in Bioinformatics |
| Master of Science in (Microbiology, Fisheries, Medical Entomology, Physics, Statistics, Biochemistry, Biotechnology, Chemistry, Botany, Immunology) |
| Master of Science in Livestock Sciences |
| Master of Science in Agribusiness |
| Master of Science in Agronomy |
| Master of Science in Geography |
| Master of Environmental Studies (Community Development) |
| Master of Environmental Sciences |
| Masters of Arts in (Kiswahili, Literature, French, English, Sociology, Religious Studies, Philosophy |
| Master of Science in Public Health |
| Masters of Education in History of Education |
| Masters of Education in Comparative Education |
| Masters of Education in Sociology of Education |
| Masters of Education in Philosophy of Education |
| Masters of Education in Economics of Education |
| Masters of Education in Educational Planning |
| Masters of Education in Educational Administration |
| Masters of Education: (Educational Psychology) |
| Masters of Education (Agricultural Education) |
| Masters of Education (Mathematics and Science Education) |
| Master of Education (Economics) |
| Master of Education (Curriculum Development) |
| Master of Education (Comparative and International Education) |
| Master of Education (Administration) |
| Master of Arts in Religious Studies |
| Master of Arts in English and Linguistics |
