Rinpoche was born north of Lhasa in 1878. In the night when he was born, a light shone in the room and people outside the house had a vision of a protector on the roof. As a child he exhibited unusual qualities and thus was taken before Sharpa Rinpoche Chuje Lobsang Dargye, one of the leading religious figures of the day. He was recognized as an emanation of the great scholar Jangya Rolpai Dorje (1717-1786), the lama of the Chinese emperor Chien Lung, although initially it was thought that he was the reincarnation of a learned Geshe from Sera-Mey Monastery. It is commonly believed that Rinpoche was also the reincarnation of Tsako Ngawang Drakpa, one of the main disciples of Tsong Khapa and founder of Dhe-Tsang Monastery. Rinpoche entered Gyalrong House of Sera-Mey Monastery at the age of 7, did the usual studies of a monk, earned his Geshe degree and spent 2 years learning at the Gyuto Tantric College. Rinpoche's root guru was Dagpo Rinpoche Jampal Lhundrub Gyatso of Lhoka.

When Pabongkha Rinpoche had finished his studies he visited Dagpo Rinpoche in his cave and was sent time into a Lam Rim retreat nearby. Dagpo Rinpoche would teach him a topic and then Pabongkha Rinpoche would goaway and meditate on it. Later he would return to explain what he'd understood : if he had gained some realization into the topic, Dagpo Rinpoche would teach him some more and Pabongkha Rinpoche would go back and meditate on that. It went on like this for 10 years.

Rinpoche had 2 main qualities : from the tantric point of view, his realization and ability to present the all tantric teachings, and from the sutric point of view, his ability to teach the entire graduated path to enlightenment, Rinpoche was also a perfect example of guru devotion. Whenever he visited his lama's monastery, Rinpoche would dismount as soon as it appeared in view and prostrate all the way to the door - which was not easy because of his build; when he left the monastery he would walk backwards until it was out of sight. Due to Rinpoche's knowledge and practice, tens of thousands of people became his disciples, including numerous eminent lamas, powerful generals and even attracting Chinese government officials and monks coming all the way from Beijing and Shanghai to Lhasa in order to receive his teachings.

Rinpoche's 4 main disciples were Kyabje Trijang Rinpoche, Kyabje Ling Rinpoche, Khangsar Rinpoche and Tathag Rinpoche. Tathag Rinpoche was the main teacher of His Holiness the 14th Dalai Lama when he was a child and gave him his novice ordination. Trijang Rinpoche and Ling Rinpoche were later appointed as the junior and senior tutors to His Holiness and Ling Rinpoche was elected to be the 97th throne holder of the Gelugpa lineage (Gadan Tripa). Khangsar Rinpoche's Chinese disciple, Master Nan Hai, started a Buddhist movement in China that survived till the present day despite political changes in Communist China, with tens of thousands of spiritual descendants and over a hundred monasteries and nunneries throughout China.

Pabongkha Rinpoche passed away in 1941. His holy body was cremated and his relics preserved in one of his monasteries, Tashi Choling in Lhasa, until it was destroyed by the communist army during the 1960's.