Kongtrül was born in Rongyab (rong rgyab), Kham, then part of the Derge Kingdom. He was first tonsured at a Bon monastery, and then at 20 became a monk at Shechen, a major Nyingma monastery in the region, later moving on to the Kagyu Palpung monastery in 1833 under the Ninth Tai Situ, Pema Nyinje Wangpo (1775-1853). He studied many fields at Palpung, including Buddhist philosophy, tantra, medicine, architecture, poetics and Sanskrit. By thirty he had received teachings and empowerments from more than sixty masters from the different schools of Tibetan Buddhism. Kongtrül studied and practiced mainly in the Kagyu and Nyingma traditions, including Mahamudra and Dzogchen, but also studied and taught Jonang Kalachakra. He also went on tour with the fourteenth Karmapa and taught him Sanskrit. He became an influential figure in Kham and eastern Tibet, in matters of religion as well as in secular administration and diplomacy. He was influential in saving Palpung monastery when an army from the Tibetan government of Central Tibet occupied Kham in 1865.