If you've decided to study at NIT Arunachal Pradesh, then you must know that it's a remote institute functioning in its temporary campus at Yupia.
You can reach the Naharlagun railway station in Andhra Pradesh in the following ways-
NIT buses are the best option according to many I know, it arrives on the main road between 8:30–9:00 am. You can take a lift from the locals or better yet, if you see any ITBP personnel, go ahead and travel with them as its headquarter is nearby. I've heard that there's a weekly train from New Delhi to Naharlagun. You can take that.