Built in 1601 on the order of the first Nguyễn lords, Nguyễn Hoàng, who at that time was the governor of Thuận Hóa (now known as Huế).
The Nguyen Lords were in name, officials of the ruling Lê Dynasty in Hanoi, but was the de facto independent ruler of central Vietnam.
According to the royal annals, Hoang while touring the vicinity, was told of the local legend in which an old lady, known as Thiên Mụ (literally "celestial lady"), dressed in red and blue sat at the site, rubbing her cheeks.
She foretold that a lord would come and erect a pagoda on the hill to pray for the country's prosperity.
She then vanished after making her prophecy.
Upon hearing this, Hoang ordered the construction of a temple at the site, thus the beginning of Thiên Mụ Tự.

The original temple was simply constructed, then later expanded and refurbished.
In 1665, major construction was undertaken by the Nguyễn Lord Nguyễn Phúc Tần.

In 1695, the Zen Master Thích Đại Sán, a member of the Tào Động sect, arrived from China.
He had been invited to come to Huế as a guest of the Nguyễn Lords to start a Buddhist congregation and oversee its development.
He was a noted Buddhist scholar of the Qing Dynasty and was patronised by the ruling Lord Nguyễn Phúc Chu and was appointed as the abbot of the pagoda.
In the seventh month of 1696, he returned to China, but conferred bodhisattva vows on Chu.

In 1710, Chu funded the casting of a giant bell, which weighs 3,285 kg, and was regarded as one of the most prized cultural relics of its time in Vietnam.
The bell is said to be audible 10 kilometres (6.2 mi) away and has been the subject of many poems and songs, including one by Emperor Thiệu Trị of the Nguyễn Dynasty who ruled in the 1840s.

In 1714, Chu oversaw another series of major expansions and construction projects, the largest expansion phase in the pagoda's history.
The main set of triple gates were erected, in addition to different shrines to the heavenly realms, the Jade Emperor, the Ten Kings, halls for preaching dharma, towers for storing sutras, bell towers, drum towers, meditation halls and halls to venerate Avalokiteshvara and the Medicine Buddha and living quarters for the sangha.

Chu also organised for the staging of the vassana retreat which occurs annually between the full moon of the fourth and the seventh lunar month.
The tradition had been inaugurated in the time of Gautama Buddha in ancient India to coincide in the rainy season.
During this time, monks would stay in one place and pursue their spiritual activities, rather than wandering around and expounding the dharma to the populace, since they were prone to step on living beings during this time due to the water covering their paths.
He also organised an expedition to China to bring back copies of the Tripitaka Canon and the Mahayana sutras, which comprised more than one thousand volumes, and interred them in the pagoda.

During the 19th century, the pagoda was patronised by the emperors of the Nguyễn Dynasty, which was founded in 1802 by Emperor Gia Long after his unification of modern Vietnam.
His successor Minh Mạng funded further expansion and renovation of the temple.

Emperor Thiệu Trị, who succeeded Minh Mạng, erected the Từ Nhân Tower in 1844, which is now known as the Phước Duyên tower.
The brick tower stands 21 m and is of octagonal shape and has seven stories, each of which is dedicated to a different Buddha.
The tower has stood there since, overlooking the Perfume River, and has become synonymous with the landscape of Huế and the Perfume River.
Its impact is such that it has become the unofficial symbol of the city.

The temple also contains a statue of a large marble turtle, a symbol of longevity.
Beside the tower on either side are structures that record the architectural history of the tower, as well as various poems composed by Thiệu Trị.

The pagoda and its buildings were severely damaged in a cyclone in 1904.
Emperor Thanh Thai authorised reconstructions in 1907 and it has continued to the current day, although it was still substantially less grand and expansive as its halcyon days
Built in 1601 on the order of the first Nguyễn lords, Nguyễn Hoàng, who at that time was the governor of Thuận Hóa (now known as Huế). The Nguyen Lords were in name, officials of the ruling Lê Dynasty in Hanoi, but was the de facto independent ruler of central Vietnam. According to the royal annals, Hoang while touring the vicinity, was told of the local legend in which an old lady, known as Thiên Mụ (literally "celestial lady"), dressed in red and blue sat at the site, rubbing her cheeks. She foretold that a lord would come and erect a pagoda on the hill to pray for the country's prosperity. She then vanished after making her prophecy. Upon hearing this, Hoang ordered the construction of a temple at the site, thus the beginning of Thiên Mụ Tự.
The original temple was simply constructed, then later expanded and refurbished. In 1665, major construction was undertaken by the Nguyễn Lord Nguyễn Phúc Tần.
In 1695, the Zen Master Thích Đại Sán, a member of the Tào Động sect, arrived from China. He had been invited to come to Huế as a guest of the Nguyễn Lords to start a Buddhist congregation and oversee its development. He was a noted Buddhist scholar of the Qing Dynasty and was patronised by the ruling Lord Nguyễn Phúc Chu and was appointed as the abbot of the pagoda. In the seventh month of 1696, he returned to China, but conferred bodhisattva vows on Chu.
In 1710, Chu funded the casting of a giant bell, which weighs 3,285 kg, and was regarded as one of the most prized cultural relics of its time in Vietnam. The bell is said to be audible 10 kilometres (6.2 mi) away and has been the subject of many poems and songs, including one by Emperor Thiệu Trị of the Nguyễn Dynasty who ruled in the 1840s.
In 1714, Chu oversaw another series of major expansions and construction projects, the largest expansion phase in the pagoda's history. The main set of triple gates were erected, in addition to different shrines to the heavenly realms, the Jade Emperor, the Ten Kings, halls for preaching dharma, towers for storing sutras, bell towers, drum towers, meditation halls and halls to venerate Avalokiteshvara and the Medicine Buddha and living quarters for the sangha.
Chu also organised for the staging of the vassana retreat which occurs annually between the full moon of the fourth and the seventh lunar month. The tradition had been inaugurated in the time of Gautama Buddha in ancient India to coincide in the rainy season. During this time, monks would stay in one place and pursue their spiritual activities, rather than wandering around and expounding the dharma to the populace, since they were prone to step on living beings during this time due to the water covering their paths. He also organised an expedition to China to bring back copies of the Tripitaka Canon and the Mahayana sutras, which comprised more than one thousand volumes, and interred them in the pagoda.
During the 19th century, the pagoda was patronised by the emperors of the Nguyễn Dynasty, which was founded in 1802 by Emperor Gia Long after his unification of modern Vietnam. His successor Minh Mạng funded further expansion and renovation of the temple.
Emperor Thiệu Trị, who succeeded Minh Mạng, erected the Từ Nhân Tower in 1844, which is now known as the Phước Duyên tower. The brick tower stands 21 m and is of octagonal shape and has seven stories, each of which is dedicated to a different Buddha. The tower has stood there since, overlooking the Perfume River, and has become synonymous with the landscape of Huế and the Perfume River. Its impact is such that it has become the unofficial symbol of the city.
The temple also contains a statue of a large marble turtle, a symbol of longevity. Beside the tower on either side are structures that record the architectural history of the tower, as well as various poems composed by Thiệu Trị.
The pagoda and its buildings were severely damaged in a cyclone in 1904. Emperor Thanh Thai authorised reconstructions in 1907 and it has continued to the current day, although it was still substantially less grand and expansive as its halcyon days
Pagoda of the Celestial Lady