The country's admission was passed by 98 percent of FIFA members at the body's annual congress in Budapest.
The president of the South Sudan football association, Oliver Mori Benjamin, reminded members that the country was "still at war" but added: "We promise that we will develop football to fight against war and hunger."
South Sudan and Sudan have been blighted by conflict. Peace talks between the two nations are due to resume next week after weeks of border skirmishes and bombardments.
(For more sports news and updates, follow Ahram Online Sports on Twitter: @AO Sports)
Short link: