Dzongsar was founded as a Sakya monastery in Derge, Kham, in 1253 by Drogon Chogyel Pakpa Lodro Gyeltsen. There was previously a Bon religious community at the site. In 1918 Dzongsar Khamshe College was constructed there by Dzongsar Khyentse Chokyi Lodro, the reincarnation of Jamyang Khyentse Wangpo. It is the seat of the Dzongsar Khyentse incarnation line.