Following is the fee structure for each masters degree program for admission in session 2019;
| S# | Programme Name | Fee |
| 1 | M. Sc Biology | 30794 |
| 2 | M. Sc Chemistry | 30794 |
| 3 | M. Sc Physics | 30794 |
| 4 | M.Sc. Environmental Science | 30794 |
| 5 | M.Sc. Mountain Area Development | 30794 |
| 6 | M.Sc. Natural Hazard Management | 30794 |
| 7 | M. Sc Behavioral Sciences | 30794 |
| 8 | M. Sc Media & Communication | 29994 |
| 9 | M. Sc Economics | 29994 |
| 10 | M. Sc International Relation | 29994 |
| 11 | M.Sc. Mathematics | 29994 |
| 12 | M. Sc Statistics | 32894 |
| 13 | MA Education / M.Ed | 32894 |
| 14 | M.Ed One Year | 44294 |
| 15 | MBA (3.5 Years) | 44294 |
| 16 | MBA Professional (1.5 Years) | 44294 |
|
17 |
M. Sc. Development Studies | 33994 |
| 18 | MA English | 44294 |
| 19 | Elementary Education (Two Years) | 29994 |