Tamiyo Taga, the leader of the BJP in the state assembly, is expected to be sworn in this morning.
On September 17, the state slipped out of Congress rule after Mr Khandu and all but one Congress lawmaker deserted the party and joined the People's Party of Arunachal, a BJP ally and a member of the North East Democratic Alliance that is a party of the NDA. Only former Chief Minister Nabam Tuki remains in the Congress.
The BJP has 11 lawmakers in the assembly.
Earlier this month, Mr Khandu reportedly met Prime Minister Narendra Modi in Delhi and invited the BJP to join his government.
The Congress's previous government led by Nabam Tuki had collapsed after the party's rebels, along with the opposition BJP, voted it out in a special session held at a makeshift venue.
After a period of central rule, Congress rebels led by Kalikho Pul took power with support from the BJP. That government lasted only five months as the Supreme Court reinstated the previous government.
Mr Pul was found hanging in his home in August.