In a phased manner considering resources and national need, graduate program will be initiated in the remaining faculties.
| S.N | College/Institute | Program | In take capacity | Duration in years |
| 1. | College of Agriculture and Veterinary Medicine | PhD in Horticulture | 5 | 3-4 |
| PhD in Plant Breeding | 5 | 3-4 | ||
| PhD in Plant Pathology | 5 | 3-4 | ||
| PhD in Animal Nutrition | 5 | 3-4 | ||
| MSc Horticulture & Plant Science | 20 | 2 | ||
| MSc Plant Breeding | 10 | 2 | ||
| MSc Plant Pathology | 10 | 2 | ||
| MSc Plant Biotechnology | 10 | 2 | ||
| MSc Agronomy | 10 | 2 | ||
| MSc Animal Production | 10 | 2 | ||
| MSc in Entomology | 10 | 2 | ||
| MSc in Natural Resources Management | 10 | 2 | ||
| MSc in Veterinary Epidemiology | 10 | 2 | ||
| MSc in Post Harvest Management | 10 | 2 | ||
| MSc in Veterinary Public Health | 10 | 2 | ||
| MSc in Agribusiness & Value Chain Management | 10 | 2 | ||
| MSc in Physical Land Resources (Specialization in Soil Science | 10 | 2 | ||
| MSc in Weed Resource | 10 | 2 | ||
| MSc in Animal Breeding | 10 | 2 | ||
| 2. | College of Health Sciences | MPH in Health Services Management | 10 | 2 |
| MPH in Epidemiology | 10 | 2 | ||
| MPH in Reproductive Health | 10 | 2 | ||
| MPH in Health Education | 10 | 2 | ||
| MPH in General Public Health | 10 | 2 | ||
| MSc in Environmental Science & Technology | 10 | 2 | ||
| MSc in Adult Nursing | 10 | 2 | ||
| MSc in Health Monitoring & Evaluation | 30 | 13 Months | ||
| MHA (Master of Health care & Hospital Administration) | 30 | 2 (For MOH) | ||
| MSc Maternity Nursing | 10 | 2 | ||
| Internal Medicine Specialty | 10 | 3 | ||
| Surgery Specialty | 10 | 4 | ||
| Pediatrics specialty | 10 | 3 | ||
| Obstetrics & Gynecology specialty | 5 | 4 | ||
| Ophthalmology Specialty | 10 | 4 | ||
| MSc in Emergency Surgery Specialty | 20 | 3 (For MOH) | ||
| MSc in Microbiology | 10 | 2 | ||
| MSc in Physiology | 10 | 2 | ||
| MSc in Parasitology | 10 | 2 | ||
| MSc in Clinical Pharmacy | 10 | 2 | ||
| Pathology Specialty | 5 | 3 | ||
| MSc in Pharmacy Administration | 10 | 2 | ||
| MSc in Clinical Laboratory Sciences | 10 | 2 | ||
| MSc in Psychiatry | 10 | 2 | ||
| MSc in Environmental Health | 10 | 2 | ||
| PhD in Environmental Health | 5 | 3-4 | ||
| PhD in Applied Ecology | 5 | 3-4 | ||
| 3. | College of Business & Economics | MBA in Business Management | 20 | 2 |
| MA in Economics | 10 | 2 | ||
| MA in Accounting and Finance | 10 | 2 | ||
| MPA(Masters of Public Administration) | 10 | 2 | ||
| MA in Accounting | 20 | 2 | ||
| 4. | College Natural Sciences | PhD in Applied Microbiology | 5 | 3-4 |
| MSc in Analytical Chemistry | 10 | 2 | ||
| MSc in Inorganic Chemistry | 10 | 2 | ||
| MSc in Organic Chemistry | 10 | 2 | ||
| MSc in Physical Chemistry | 10 | 2 | ||
| Masters in Bio-statistics | 10 | 2 | ||
| MSc in Chemistry | 10 | 2 | ||
| MSc in Applied Microbiology | 10 | 2 | ||
| MSc in Botanical Sciences | 10 | 2 | ||
| MSc Ecological and Systematic Zoology | 10 | 2 | ||
| MSc in Mathematics | 10 | 2 | ||
| MSc in Information and Knowledge Management | 10 | 2 | ||
| MSc in Electronic and Digital Resource Management | 10 | 2 | ||
| MSc in Astrophysics | 10 | 2 | ||
| MSc in Condensed Matter | 10 | 2 | ||
| MSc in Quantum Optics | 10 | 2 | ||
| MSc in Sport Management | 10 | 2 | ||
| MSc in Foot Ball | 10 | 2 | ||
| 5. | College of Social Sciences and Humanities | MA in TEFL | 15 | 2 |
| MA in History | 10 | 2 | ||
| MA in History and Heritage | 10 | 2 | ||
| MA in Counseling Psychology | 10 | 2 | ||
| MA in Engish Literature | 10 | 2 | ||
| MA in Educational Psychology | 10 | 2 | ||
| L.L.M in Commercial and Investment Law | 10 | 2 | ||
| MA in Oromo Folklore and Cultural Studies | 10 | 2 | ||
| MA in Applied Linguistics and Ethiopian Language and Cultural Studies | 10 | 2 | ||
| MA in Governance and Development Studies | 10 | 2 | ||
| 6. | Jimma Institute of Technology | MSc in Sustainable Energy Engineering | 10 | 2 |
| MSc in Structural Engineering | 10 | 2 | ||
| MSc in Water Resource Engineering | 10 | 2 | ||
| MSc in Environmental Engineering | 10 | 2 | ||
| MSc in Electrical Power Engineering | 10 | 2 | ||
| MSc in Geotechnical Engineering | 10 | 2 | ||
| MSc in Construction Engineering & Management | 10 | 2 | ||
| MSc in Hydraulics Engineering | 10 | 2 | ||
| MSc in Communication Engineering | 10 | 2 | ||
| 7. | College of Education & Behavioural Science | MA in Educational Leadership | 10 | 2 |
| MA in Curriculum and Instruction | 10 | 2 | ||
| MA in Adult Educational and Life Long Learning | 10 | 2 |