Swayambhu is not only one of the most honorable Buddhist sites of the Kingdom but also the most sacred of the Kathmandu valley, as it symbolizes the creation of the valley itself.
As mentioned in the Savayambhupurana, the present day Kathmandy valley used to be a lake called Kalihrada. In Satyayuga Bipaswi Buddha sowed a lotus seed in the lake and after eighty thousand years the lotus bloomed. Self-Existent Lord, the Swayambhunath manifested himself in the form of Light (Jyotirupa) from this lotus.
In Treta Yuga, the Bodhisattva Manjusri came from China to pay the pilgrimage. He found the access to Swayambhu difficult due to monstrous aquatic animals in the lake. With his sword he cut the mountain surrounding the lake at a place called Kotbar (Chobar) and drained the water. The valley then became a place for human settlement, known as Manju Pattan. Latter the disciplines of Manjusri built the Manjusri Chaitya near the Swayambhu Mahachaitya to his memorial.
Later in Dwapar Yuga, the Bodhisatva Vajrasattva fearing that wicked men in the age of Kaliyuga would steal away the jewels of Swayambhu concealed him under a stone salb. Master Santikaracharya raised a chaitya over the hidden Swayambhu, which remained there until today.
The historical evidence of the Swayambhunath as religious site goes back to early Lichhavi time (5th century AD) attested to by the inscriptions as well as two chaityas from the period. More chaityas seems to be constructed in the latter part of Lachhavi period survive, six on the hill top and three along the eastern stairs.
Pratapa Malla was the only king who contributed larger buildings to the immediate surroundings of the Swayambhu Chaitya (2) . He not only placed the enormous Vajra at the head of the Eastern stairs, but added a pair of Sikhara temples right and left of the stairs. The southern one, Pratapapura bears his name.
For centuries Swayambhu Chaitya has not been in a good state of repairs. The earliest recorded renovation of the chaitya is from 1129 AD. The existing structural form of the Chaitya dates from the renovation carried out in 17th century. After Countless renewals and additions the central building got its present shape only 60 years ago.