Thapa will fly to New Delhi on June 10, Foreign Ministry sources here said.
During his four-day visit, Thapa, who is also Nepal's Foreign Minister, is expected to meet Swaraj and top officials.
Thapa's visit comes at the invitation of South Asian University which is organising its convocation on June 11 in New Delhi.
This will be Thapa's fourth visit to India since he assumed office in October last year.
Around 450 students will be receiving their degrees at the convocation.