As per the historical accounts, Bumthang region was under the rule of King Sindu Raza in the 8th century. During the King’s reign, he was struck with terrible illness. He was supposedly cursed by the local guardian deity Shelging Karpo. Upon the King’s invitation, Buddhist saint Guru Rinpoche is believed to have travelled to Bumthang. Guru Rinpoche meditated in a cave to subdue the evil spirits and the King’s health was restored. Imprints of Guru Rinpoche’s body remained in that cave and hence the name Kurje (imprint of the body).

In 1652, first Governor of Trongsa constructed the oldest Lhakhang enclosing the cave. Today there are three main Lhakhang at Kurje. It is also believed that the cypress tree near the entrance is an offshoot of Guru Rinpoche’s walking stick.