President Salva Kiir held a private meeting with the Pope during a visit to Uganda.
The meeting with Pope Francis lasted about 20 minutes at Uganda's State House in Entebbe.
The meeting on Friday was arranged by Uganda President Yoweri Museveni.
Presidential Press Secretary Ateny Wek Ateny told Radio Miraya that the Pontiff passed a message of peace and reconciliation to the people of South Sudan.