Dr. Sally Samuel Lolako was appointed on May 25, 2011 to oversee the national team. The national team's first international fixture was due to be against the Kenyan national team on 10 July 2011 as part of the country's independence celebrations. However, in the event the opposition was provided by Tusker FC of the Kenyan Premier League, alongside the first international fixture of the national basketball team. The match was played at Juba Stadium. South Sudan scored within ten minutes, but they later conceded three goals in a 3–1 defeat. South Sudan was officially admitted as a CAF member on 10 February 2012, at the 34th CAF Ordinary General Assembly hosted in Libreville, Gabon. South Sudan was admitted as a FIFA member on 25 May 2012 at the second session of the 62nd FIFA Congress hosted in Budapest, Hungary.
On 10 July 2012, South Sudan competed in its first full international match, a friendly against Uganda in Juba. The match ended in a 2-2 draw, with James Moga and Richard Justin Lado scoring for South Sudan. This match resulted in South Sudan entering the FIFA rankings at the start of August in 199th place.
The South Sudanese took part in their first ever international football tournament when they took part in the 2012 CECAFA Cup in Uganda. They were drawn in Group A alongside Ethiopia, Kenya, and hosts Uganda. The national team played their first match against Ethiopia, losing 1-0 through a Yonathan Kebede goal. In their next match, they lost 2-0 against Kenya. Their final match saw them suffer a 4-0 loss to Uganda.
South Sudan entered its first major international tournament in 2014, taking part in the 2015 Africa Cup of Nations qualification. As one of the four lowest ranked national teams in Africa, it entered in the preliminary stage and was scheduled to play against Eritrea, who withdrew, thus qualifying South Sudan for the first qualifying round. There, the played Mozambique over two legs, losing a national record 5–0 at the Estádio do Zimpeto in Maputo, but hosting a goalless draw in the second leg despite being eliminated on aggregate. South Sudan's home leg was held at the Khartoum Stadium in Sudan due to the South Sudanese Civil War.
In international football, players can normally only play for one national team once they play in all or part of any match recognised as a full international by FIFA. However, an exception is made in cases where one or more newly independent states are created out of a former state. Based on current FIFA rules, a player will be eligible to play for South Sudan, even if he had previously represented Sudan or any other country, if at least one of the following statements applies:
He was born in South Sudan.
At least one of his parents and/or grandparents was born in South Sudan.
He has lived in South Sudan continuously for a two-year period.