You need to clear GPAT exam first and then you would be eligible for NIPER entrance exam. If you qualifies NIPER exam (MCQ based) then you have to opt for MBA(Pharm) and appear for GD. Based on GD there would be a list of candidates released for counselling. Finally on counselling day, you can deposit the admission fee if your name appears on the list and sufficient number of seats are available.

You can also check in NIPER entrance form if there is a provision to select the option for MS(Pharm) and MBA(Pharm) in the beginning.