He will perform the prayer at the main temple situated on the banks of river Bagmati on the outskirts of Kathmandu on Monday by giving a bath of 'panchamrit' to Shiva Linga.
Modi will get 'prasad' from chief priest Ganesh Bhatta, who hails from south India. There is a tradition of keeping four priests and one chief priest at the temple from among the Bramhins of south India for centuries.
A group of 21 Bramhins will chant Rudri, a holy script, as the chief priest performs the prayer, according to Govinda Tandon, chief of the Pashupati Area Development Trust which manages the temple's affairs.
Modi will also offer prayers at Basuki temple situated in the southern side of the main temple.
As soon as Modi arrives, 108 young Bramhin students of Vedavidyashram located near the temple, will chant Vedic hymns to welcome him.
Dhime, traditional Newari drum and Bansuri, Nepali flute will also be played to welcome the distinguished guests.
He will worship around two dozen idols placed in the Pashupatinath temple complex.
On the occasion, Modi will be presented a replica of Pashupatinath Temple by its authorities.
The temple, listed in UNESCO World Heritage Sites, is one of the most significant Hindu temples of Shiva in the world.
As per Hindu calendar, Mondays of the month of Shrawan are considered auspicious, when around 300,000 people from Nepal and India visit the temple, according to authorities.
Last week, External Affairs Sushma Swaraj visited the temple. During her visit a Rs 250-million assistance package was announced for the preservation of the temple.
India has also offered to provide 2,500 kg of Shrikhanda (Sandalwood) worth Rs 2 crore for the temple.
A 400-bed 'dharamshala' is also being built inside the temple premises with assistance from India.