The Gilgit manuscripts were first discovered at the ruins of an ancient stupa-like structure at Naupur village in Gilgit in 1931. It was a chance discovery made by a group of young shepherds some two miles west of Gilgit in Kashmir. The manuscripts were found inside a wooden box at the site. Excavations at the site were undertaken in 1938 and numerous manuscripts were unearthed. Although the original function of the building is not known it is believed to be a monastery library for Buddhist monks who possibly served as religious advisers, ritual practitioners, healers, copyists and scribes.

The unearthed manuscripts have not been preserved as a whole but they have been scattered in various libraries across the world. The British archaeologist Aurel Stein took some manuscripts to the British Museum while Joseph Hackin, the French archaeologist deposited some at the Musée Guimet in Paris. A major portion of the manuscripts was kept at the Srinagar Museum by the Maharaja of Kashmir. During the 1948 India-Pakistan war, the then Prime Minister of India, Pandit Jawaharlal Nehru had a portion of the manuscripts at Srinagar airlifted to New Delhi. 

It has become impossible at present to determine the total number of texts or titles that were preserved at the site. However, it has been estimated that there were approximately 50 manuscripts which contained 57 titles along with 17 Avadanas (stories that deal with karma which are usually narrated by the Buddha). 

These manuscripts were earlier only known through their Chinese and Tibetan translations. The discovery of the Sanskrit originals at Naupur was a momentous event in Buddhist textual history. One of the most prominent of the Gilgit manuscripts are the Saddharmapundarikasutra (the Lotus Sutra) manuscripts and four of these are preserved at the National Archives in New Delhi. 

The Gilgit manuscripts of the Saddharmapundarikasutra are written on birch bark with the exception of one which is written on clay-coated paper. This particular manuscript is the only one of the Gilgit manuscripts which is entirely written on this kind of paper. A few Gilgit manuscripts like the Samghatasutra are written partially on birch bark and partially on such clay-coated paper. These manuscripts were well-preserved on account of the cold temperatures of the Gilgit region and the birch bark which is known for their resistance to decay and decomposition.

The colophons (printer's emblem on the title page of a book) of most Gilgit manuscripts are not preserved. Only two Saddharmapundarikasutra manuscripts have intact colophons. These colophons are of immense historical importance as they have the names of the donors of the manuscript inscribed on them. These persons have also been recognized as the first worshippers of the Saddharmapundarikasutra. From the information presented in these colophons, it can be assumed that the custom of reciting the names of deceased donors was practised in Gilgit which resulted in the donors being remembered for a long period of time.