Governor Tathagat Roy administered him the oath of office and secrecy at a function in Itanagar. Chawna Mein was swon-in as Deputy Chief Minister.
Mr Khandu represents Moktu assembly constituency in Tawang district. He is the son of former Chief Minister Dorjee Khandu.
Earlier, Nabam Tuki resigned as Chief Minister of the state paving the way for Mr Khandu to take over the CM's post.