He will call on President Sirisena, who will also host an official lunch on Tuesday.
Lee will also meet his Sri Lankan counterpart Ranil Wickremesinghe and receive a courtesy call from the leader of the opposition, R Sampanthan.
During the visit, Mr Lee will witness the signing of the Sri Lanka-Singapore free trade agreemen.
Lee is being accompanied by Mrs Lee, Minister for Foreign Affairs Vivian Balakrishnan, Minister for Trade and Industry (Industry) S Iswaran and other Government officials.
He will then visit New Delhi from Wednesday to Friday to attend the ASEAN-India Commemorative Summit.