Lungtaen Gyatso studied Buddhism initially at the Ngagyur Nyingma Institute in Mysore, and later at the Sikkim Higher Nyingma Studies, Gangtok, Sikkim, India, from where he graduated in 1989. In 1990 he started his Sanskrit Literature studies at the Sampurnand Sanskrit University, Varanasi, UP, India, from where he graduated in 1997. In 1997-98 he worked with Sanskrit Bharati, a non-governmental organization in New Delhi.

He also worked with the State Council for Research and Training (SCRT) State Government of Delhi, New Delhi in training the Delhi Government School Sanskrit Teachers to teach Sanskrit through Sanskrit language. Parallel to his academic career he worked as a visiting lecturer in the Darthang Nyingma Shedra in Kathamandu, Nepal from 1990 to 1993. He joined the Institute of Language and Culture Studies (now a constituent college of the Royal University of Bhutan) in 1999 as a lecturer. Currently he is serving as the Director of the same institute.