Beijing views the Dalai Lama as a dangerous separatist campaigning for Tibetan independence and consistently condemns foreign leaders who meet him.
Botswana “will be extending the normal courtesies for visiting dignitaries”, the government said Wednesday in a statement.
“His Excellency (President Khama) will meet the Dalai Lama when he is in Botswana.”
The Tibetan spiritual leader, who lives in exile in India, is due to make a public address at the three-day “Mind and Life Dialogue” conference in the Botswana capital Gaborone on August 19.
Botswana’s neighbour South Africa has repeatedly denied the Dalai Lama a visa in an apparent attempt to further boost ties with China, drawing fierce criticism from archbishop Desmond Tutu and others.
China’s growing demand for raw materials has seen a rapid rise in trade with Africa.
The Chinese government has helped build coal-powered power plants, road networks, bridges and schools in Botswana, in some of its many infrastructure projects in Africa.
Many in the continent see Beijing as a counterbalance to the West, but the relationship has also raised accusations of neo-colonialism.
Botswana, one of the world’s largest diamond producers, has a population of just two million people and is known for its stable political scene.
A government spokesman declined to comment to AFP on any risk to relations with China.
The Dalai Lama says he seeks more autonomy for Tibet rather than outright independence.
“Botswana, I am really excited,” he said in a video clip on the conference website.
“I am looking forward to come there, to participate and in the meantime see my African brothers and sisters.”
The website, which offers tickets ranging from $25 to $500, said Khama would give the opening speech at the conference.
China has made no immediate comment on the visit.