Thapa was born in Dehradun, Uttarakhand, where he started his schooling at St. Joseph's Academy. He began playing football at the age of 10 at the St. Stephen's Football Academy in Chandigarh. After spending time with the India U14 side, he was selected to join the AIFF Regional Academy in Kalyani in 2012. As he moved up the national youth team ranks, Thapa moved into the AIFF Elite Academy where he became captain of the side in the I-League U19. In April 2016 Thapa, along with four other players, was selected to join French Ligue 2 side Metz on a short training-stint which was sponsored by Indian Super League side Chennaiyin.
