Before becoming Tsongkhapa's foremost disciple, Khedrup Je had been a learned Sakyapa scholar. He is considered to be a reincarnation of Manjushri, the god of Wisdom. He wrote an important text on Kalachakra Initiation which is still used by Tenzin Gyatso, the 14th Dalai Lama, as the basis of his public initiations into the Kalachakra. Altogether, there are nine volumes of his Collected Works, containing fifty-eight treatises.
Khedrup was posthumously decided to have been a previous incarnation of Lobsang Chökyi Gyaltsen (1570-1662), and is considered to be the First Panchen Lama and, like all the Panchen Lamas, was an incarnation of Amitabha Buddha.
Khedrup Je was unanimously chosen as Ganden Monastery's third abbot (after Tsongkhapa and Gyaltsab Je) by its monks, and also became the Ganden Tripa, the leader of the Gelug tradition. Khedrub Je was a prolific writer (for example on Kalachakra), and founded Baiju Monastery in Gyantse District in Tibet in 1418. He also wrote many prayer books.
According to the legend, after Tsongkhapa passed away in 1419, his disciple Khedrub Jey on five occasions met with him in mystical states. Kedrub Jey is most remembered for his charisma as a teacher, as well as for the many excellent commentaries that he wrote on the tantric lineages which Tsongkhapa gathered together and elucidated. He played an important role in the education of the First Dalai Lama, who was the youngest of Tsongkhapa's five chief disciples.