This monastery is situated on the summit of the hill above Gyalzing bazaar, West Sikkim. History: It was originally started with a small Shrine called ‘Tsangkhang’ founded by Lhatsun Chhenpo on a spot due west of the present Monastery probably between 1650 to1651 A.D, or almost at the same time in the founding year of the Sang-ngag Choling monastery.

Later, Chhogyal Chhagdor Namgyal and Lama Khanchhen Rolpai Dorje (First Head Lama of Pemayangtse Gonpa) shifted this Lhakhang to its present site and re-established it in 1705 A.D. with tremendous increase in its size. The new Monastery was named as “Sangchhen Pemayangtse Gonpa” (Most Secret Lotus Summit- Monastery) and was started with an enrolment of 108 monks from the family of pure descents with the king himself enrolled as the first number. The Pemayangtse was specially built for the pure celibate and physically sound monk called ‘Dra-tsang’ and to its Lama was reserved the honour of anointing and crowning the Chhogyals during the time of the Monarchy rule.
In 1965, due to its old age, the  upper portion of the monastery structure was further renovated with Government aid by the lamas . At that time, the old structure of Sangdogpalri in the first floor of the monastery was dismantled during the renovation. However, it’s reinstallation was entrusted to late Serdup Dungzin Rinpoche, Jigme Wangchuk, who started the work on 23rd November 1967 with addition of many more missing items and brought it to full completion in the year 1972. "Sangdogpalri " the Guru Rinpoche's Heavenly abode, which is a beautiful wooden masterpiece, is the main attraction of this Monastery. His Holiness Dudjom Rinpoche, the Supreme Head of the Nyingmapa Sect, in 1972, imparted the consecration of this restored masterpiece.
A small lhakhang near the entrance contains a statue of Dorje Phagmo (Vajra Varahi) which was presented to Chogyal Gyurmed Namgyal by Terton Terdag Lingpa of Tibet as a gift when he married his daughter. This statue is considered to be very sacred due to its association with the great Lama who was considered to be a master of Nyingma School of Tibetan Buddhism and whose student Jigmed Pawo established the monastery at present site. Its main festival is Guru Drakmar Chham in winter corresponding to the month of February-March. Pemayangtse Monastery has more than 100 monks at present and is a parent Monastery of all the monasteries following the Mindroling lineage in Sikkim.