The monastic complex was originally founded in 1243 when Sakya Pandita Kuenga Gyaltshen (kun dga' rgyal mtshan, 1182-1251) sent an eminent monk named Shabdrung to spread his teachings in eastern Tibet. Some time later the Sakyapa patriarchs were instituted as the secular rulers of Tibet. Sakya Pandita's nephew Phagpa who had so far lived in the Mongol-Chinese capital, returned to Tibet in 1265 and during his journey is said to have stayed in Wara.

       Since 1984 Wara Gompa has undergone considerable restoration work. Now it has two large temple halls and a tulku residence rising above the houses of the monks, covering an area of 3.5 hectares.

       The main hall is called Gunggara, standing on the right if seen from the front side. Also called Yarne Lhakhang (g.yar gnas lha khang), it is the old assembly hall wherein a hundred old thangkas are said to have survived the 1960s' iconoclast. The large front courtyard has unusual murals depicting Gesar and his henchmen, embroiled in the many bloody battles as described in the famous epic songs. On the side walls of the courtyard we can also make out some mountain deities such as Nyenchen Thanglha, Machen Pomra and Tashi Tseringma. The vestibule at the dukhang's main entrance depicts the ubiquitous four lokapalas and a bhavacakra, but in addition has murals of a skull-crowned Vajrapani, of Amitabha, Green Tara, Kubera and two protector deities. The main image of the inner sanctum is a Shakyamuni statue which is said to have been donated by Phagpa upon his visit here. Another bronze statue of Shakyamuni is said to have come from India nearly one millenium ago.

        To the left of Yarne Lhakhang rises the newly built Lhakhang Sarmo (lha khanggsar too), which was not yet completed by 1997. None the less it has already quite a number of beautiful murals. The wooden boards near the skylight portray Marpa, Trisong Detsen, Atisha, Padmasambhava, a dakini, Sakya Pandita, Vajradhara, Milarepa, several Sakya lamas, Kuenga Legpa and Tsongkhapa. This mixture of lamas and gurus of different Tibetan Buddhist orders testifies to the influence of the 19th century's Rime (ris med) movement which originated in the area. It was an attempt to create 'a synthesis of academic and shamanic aspects of Tibetan religion that maintained the academic tradition but retained a much more central place for the shamanic vision than the Gelugpa synthesis allowed.' (G. Samuel) Rime lamas come from Nyingmapa, Sakyapa and Kagyuepa monasteries but stand for overcoming the sectarian divisions among the various Tibetan-Buddhist traditions. They do not reject one path in search for enlightenment in favor of another, but tend to 'maintain all paths possible as options that might be suitable for particular students.' As accordingly the central aspect of Rime was to bring the numerous diverse traditions of Yantric yogic practice together, this was expressed as well iconographically, as it has done here in Wara Gompa's 'New Temple'. The lower parts of the walls were just about being painted in 1997. The left side depicts Vairocana, Heruka, Yamantaka and Hevajra, while Kalacakra, Cakrasamvara, Guhyasamaj a, an 11-headed and 8-armed Avalokiteshvara, Amitayus, and Aksobhya are on the right wall. The main statue of the altar rises up to between 7 and 8 m high. It is a Jowo-Shakyamuni, flanked by Maitreya, Padmasambhava and Hevajra to the left, and Avalokiteshvara, Yamantaka, and Vajrapani, again with a crown of skulls, to the right.

        During the 20th century Wara Gompa had its own woodblock edition of the Kanjur prepared, which was done under the guidance of Jamyang Khyentse Choekyi Lodroe (1893-1959) of Kathog monastery. Here again we can discern the close contact between the different traditions, as the rimpoche of the latter lamasery was a Nyingmapa master while the monks of Wara Gompa adhere to the Sakyapa tradition. All in all, Wara monastery possesses eight sets of the Kanjur and the Tanjur scriptures. They will be taught and studied intensively after the completion of the study faculty which was still awaiting final fixtures and fittings in 2002.