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.