His special chartered aircraft landed at the Tribhuvan International Airport here where Nepal Prime Minister Sushil Koirala, senior ministers and Indian Ambassador Ranjit Rae received him.
Indian National Security Advisor Ajit Doval, Indian Foreign Secretary Sujatha Singh and other senior Indian officials also welcomed him.
On his arrival, Modi received the guard of honour from the Nepal Army and the national anthems of both countries wwere played.
Modi then left for Hotel Hyatt where he will be staying. Nepal's Foreign Minister Mahendra Bahadur Pandey will brief him later in the day.
On Saturday, Modi said he was "excited" about his visit that reflects the two nations' "shared heritage of nature, history, culture, spiritualism and religion".
The visit is part of the new government's initiative to forge closer ties with the neighbouring countries and comes two weeks after Modi visited Bhutan, which was his first bilateral visit after he was sworn-in as the prime minister.