Jamyang Namkha Gyaltsen was born in 1398. His father was Kunga Gyaltsen and mother was Mahick Namkha Gyalmo.

As a child, he had a prodigious capacity for learning. He memorized a 200-page text known as the Two Analyses within two days. Therefore, he earned the title of Jamyang Chenpo, or Great Mañjuśrī. He was also said to be an emanation of Padmasambhāva.

He was enthroned as the eighteen Sakya throne holder in 1421. He is also the fifteenth holder of the Vajrayoginī Lineage.