Below is the fees Structure for Muni University Uganda
| SN | FEES | PAYABLE | PAYABLE PER | PAYABLE PER | TOTAL IN |
| ONCE | ANNUM | SEMESTER | UGX PER YR | ||
| 1 | Registration Fee | 30,000 | 60,000 | ||
| 2 | Development Fee | 100,000 | 100,000 | 100,000 | |
| 3 | Technology Fee | 100,000 | 100,000 | 100,000 | |
| 4 | University Rules Fee | 10,000 | 10,000 | 10,000 | |
| 5 | Undergraduate Gown Fee | 16,000 | 16,000 | 16,000 | |
| 6 | Identity Card Fee | 25,000 | 25,000 | 25,000 | |
| 7 | UNSA Fee | 2,000 | 2,000 | 2,000 | |
| 8 | Examination Fee | 80,000 | 160,000 | ||
| 9 | Library Fee | 20,000 | 20,000 | ||
| 10 | Research Fee | 20,000 | 20,000 | 20,000 | |
| 11 | Guild Fee | 30,000 | 60,000 | ||
| 12 | Medical Examination Fee | 20,000 | 20,000 | 20,000 | |
| 13 | Medical treatment Fee | 20,000 | 20,000 | ||
| 14 | Internship Fee | 75,000 | 150,000 | ||
| 15 | Sports Fee | 15,000 | 30,000 | ||
| TOTAL FUNCTIONAL FEES PAYABLE | 563,000 | 793,000= | |||
| Other Fees | |||||
| 16 | Application Fee | 50,000 | 0 | ||
| 17 | Late Registration (Surcharge) Fee | 20,000 | 20,000 | ||
| 18 | Transcript Fee | 20,000 | 20,000 | ||
| 19 | Transcript Certification Fee | 20,000 | 20,000 | ||
| 20 | Certificate Fee | 20,000 | 20,000 | ||
| 21 | Graduation Fee | 40,000 | 40,000 | ||
| 22 | Convocation Fee | 20,000 | 20,000 | ||
| 23 | NCHE Fee | 20,000 | 0 | ||
| 24 | Retake (per paper) | 6,000 | 6,000 | ||
| 25 | Re-Examination Fee | 200,000 | 200,000 | ||
| TOTAL PAYABLE | |||||
