The tuition and fees of GJU graduate programs are classified as follows:
- An admission fee of (120 JDs) is payable once only.
- Registration fee of (120 JDs) per semester.
- Computer fee of (60 JDs) per semester.
- Medical Insurance fee of (50 JDs) per semester.
- Refundable fee of (150 JDs) is payable once only.
- The fees of credit hours are as follows:
| Master Program | Number of Credit Hours | Fees/Credit Hour |
| Master of Business Administration | 42 | 250 JD |
| Master of Social Work / Migration and Refugees | 36 | 120 JD |
| Ma DAF German as a Foreign Language | 40 | 120 JD |
| Master of Science in Spatial Planning | 36 | 120 JD |
| Master of Science in Architectural Conservation | 40 | 120 JD |
| Master of Science in Computer Engineering | 33 | 120 JD |
| Master of Science in Enterprise Systems Engineering | 33 | 120 JD |
| Master of Science in Environmental and Renewable Energy Engineering | 34 | 120 JD |
| Master of Science in Logistics Management | 36 | 200 JD |
| Master of Science in Engineering Management | 34 | 200 JD |
| Master of Science in Humanitarian WaSH (Water, Sanitation and hygiene) | 36 | 185 JD |