A special plane carrying Modi landed at the technical area of Srinagar airport around 2.10pm.
Governor NN Vohra, chief minister Omar Abdullah and senior ministers received the prime minister.
Members of flood-affected families, traders and members of the civil society will meet Modi at the Raj Bhawan.
He will also meet politicians from the ruling National Conference, the opposition Peoples Democratic Party and other mainstream parties.
He is likely to visit Rajbagh locality in Srinagar which suffered massively in the September floods.
The prime minister is also scheduled to visit a relief camp meant for flood affected families.
He will review relief and rehabilitation work by the state and central agencies.
Modi began his Diwali visit to Jammu and Kashmir from the Siachen Glacier where he met soldiers guarding the world’s highest battlefield.