According to a holy book, which was once discovered long ago, the site of the temple was once a forked piece of stone, which spouted fire. This was quite significant when the rest of the world was covered with snow and before long there emerged a five-colored flame, which came to be the volcanic goddess. The goddess ordered that a temple be built on the sight of her emergence and priests have been making use of the nine surrounding caves for centuries to serve this temple ever since. The first priest to serve here was supposedly given superior enlightenment and Bajrayogini is considered to be one of the wisest and strongest gods able to grant this gift. There is a beautiful water tap complete with decorative statue in the area, which dates back to the fourth century.The attraction here is not only the various temples but also the many other interesting temples and caves which surrounding it – some of which are considered to be older than the temple itself. Amongst the caves in the area is a carved double chamber with window attributed to being used by Marpa Lotsawa. Whereas nearby is a tiny chamber built into a small cliff which was where Milarepa was walled in for solitary retreat.
The hill top is accessed by a very long carved stone stairway. The entire site is covered richly with Newari architectural metal work, carved wood details, and ancient artifacts. Including a small stupa claimed to pre-date Buddha Shakyamuni.
The earthquake that struck on 25 April 2015 had immense effect on Sankhu city. Bajrayogini temple was no exception. The temple is marked unsafe by the engineers .Renovation of the temple is necessary in order to assure safety. The statues of Bajrayogini temple are safely shifted and the temple is supported with wooden planks.