Dear aspirant,

Yes you will have to pay the course fee. The stipened is designed in such a way that they will be just enough to get you through the MTECH courses of an NIT or IIT that's the sad part. I asked the same question to a few friends who gave gate and this is what they also said

"GATE qualified students,if pursue M.tech in colleges recognised by AICTE, get a stipend of ₹12400 monthly.They cannot claim any other fee reimbursement"

SO yeah no other fee reimbursement. 

hello aspirant ,

firstly congratulation that you have qualified GATE exam!  for details about fee structure for M. Tech kindly refer below link :

https://www.inspirenignite.com/fee-structure-and-scholarships-for-master-of-engineering-degree-m-e-m-tech-in-different-universities/

Hope this will help you !
Wish you all the best !