He made his debut for the Burkino Faso on 7 October 2006 at the age of 19. He played the entire 90 minutes where Burkino Faso defeated Senegal 1:0 in the Africa Cup of Nations Qualification. He was the member of the Burkino Faso squad that played in the 2013 Africa Cup of Nations. He played the entire minutes in the tournament and Burkino Faso became the runners up of the tournament for the first time in the history. In the final he won the Fair Player of the Match Award. On 14 November 2014, Bakary Koné captained his national side for the first time in an African Nations Cup Qualification match against Angola. With 83 appearances, Koné is currently the third most capped player for his country.