Mr Thapa, a sitting MLA and a former minister lost to Mr Rai by 2,968 votes.
Sikkim BJP president Dilli Ram Thapa lost to SKM nominee Kala Rai in the Upper Burtuk assembly constituency, officials said on Sunday.
Mr Thapa, a sitting MLA and a former minister lost to Mr Rai by 2,968 votes.
Mr Rai polled 6,723 votes while Mr Thapa got 3,755.
Sikkim Democratic Front's DB Thapa polled 1,623 votes, while BK Tamang (CAP-A) bagged 581 votes.
Polling for the 32-member Sikkim Assembly was held on April 19 along with the first phase of the Lok Sabha elections.
The counting of votes for the 32-member Sikkim Assembly started at 6 am on Sunday.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)