The monastery, now a major teaching and retreat center of the Southern Drukpa Lineage of the Kagyu school of Tibetan Buddhism, is located at the northern end of the Thimphu Valley about 15 kilometres (9.3 mi) from the capital.

In the 13th century it was visited by Phajo Drugom Zhigpo the Tibetan Lama who first established the Drukpa Kagyu tradition in Bhutan.

Samding Dorje Phagmo Chagri Dorjeden was the first monastery established in Bhutan by Ngawang Namgyal in 1620 when he was 27 years old.

These monks and the lay devotees, who gathered in Cheri, were taught by Lhawang Lodoe, who passed down the Drukpa teachings transmitted to him by Pema Karpo.

At the age of 33, he sent out edicts bearing his emblem of Ngachudruma, declaring 'all gods, humans and spirits of the Lhomonkhazhi, from this day, fall under the dominion of the great magician Nagwang Namgyal and everyone must heed to his words'.