Kiir is a Dinka, though of a different clan than former Southern Sudan president John Garang. In the late 1960s, Kiir joined the Anyanya in the First Sudanese Civil War. By the time of the 1972 Addis Ababa Agreement, he was a low-ranking officer. In 1983, when Garang joined an army mutiny he had been sent to put down, Kiir and other Southern leaders joined the rebel Sudan People's Liberation Movement (SPLM) in the second civil war. Kiir eventually rose to head the SPLA's military wing.

After the death of Garang in a helicopter crash on 30 July 2005, he was chosen to succeed to the post of First Vice President of Sudan and President of Southern Sudan. He is popular among the military wing of the SPLM for his battlefield victories and among the populace for his unambiguous pro-secession stance.

Kiir was re-elected with 93% of the vote in the 2010 Sudanese election.