Modi will most probably arrive in Janakpur on November 25 via land route and then fly to Kathmandu to attend the SAARC Summit, foreign ministry spokesperson Khagnath Adhikari said.
He will then travel on a helicopter to visit Muktinath, situated in the mountainous Mustang district in northern Nepal near the Tibet border.
On his way back to India, Modi will pay a visit to Lumbini, the birth place of Lord Buddha, situated in Nepal close to its border with India.
The temple of Lord Shiva is situated at the site. Muktinath is also famous for Buddhist pilgrimages as famous Buddhist monasteries are located there.
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Modi will make public appearances at the three religious sites and also offer prayers. He is also expected to give public speeches at these sites, though detailed itinerary has not yet been finalised, the Foreign Ministry official said.
Security has been beefed up at the religious sites outside Kathmandu.
Integrated security plans have been implemented at the sites with the help of Nepal Army, Nepal Police and Armed Police personnel.
The City Hall, situated in the heart of the city, which can accommodate about 1,000 people, is being renovated to host the main event of the regional meet.
In Kathmandu, security has been stepped up with night patrolling and deployment of more security personnel in sensitive areas.
The SAARC Summit will be held from November 26-27.