Sudanese civil warsIn 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 Dr John 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. Dr Garang De Mabior had advance military knowledge and experience from both the United States and the Sudan. President Kiir was his Deputy. Kiir eventually rose to head the SPLA, the SPLM's military wing when Dr. John Garang was killed in an helicopter crash. Rumours to remove Kiir from his post as SPLA Chief of Staff in 2004 nearly caused the organization to split.
South Sudanese politicsFollowing the signing of the Comprehensive Peace Agreement formally ending the war in January 2005,Dr John Garang was Sworn in the Vice President of the Republic of Sudan. After the death of Dr John Garang in a helicopter crash on 30 July 2005, Kiir was chosen to succeed to the post of First Vice President of Sudan and President of Southern Sudan. Before independent, Kiir was popular among the military wing of the SPLA/M for his loyalty to the vision of the SPLA/M throughout the liberation struggle and among those who do not trust the successive governments that have come and go in the Sudan.
Comments by Kiir in October 2009 that the forthcoming independence referendum was a choice between being "a second class in your own country" or "a free person in your independent state" were expected to further strain political tensions. Reports in January 2010 that Kiir would not contest April elections for Sudanese president, but would focus on re-election as president of Southern Sudan were interpreted to mean that the SPLM priority is independence.
Kiir was re-elected with 93% of the vote in the 2010 Sudanese election. Although the vote on both the national and sub-national level was criticized by democratic activists and international observers, the overwhelming margin of Kiir's re-election was noted by some media as being "Step One" in the process of secession. Following his re-election, Omar al-Bashir reappointed Kiir as the First Vice President of Sudan in accordance with the interim constitution.
President of South SudanSouth Sudanese voted overwhelmingly in favor of independence from Sudan in January 2011, with 98.83% of voters reportedly preferring to split from the North. On 9 July 2011, South Sudan became an independent state, with Kiir as its first president. Kiir positioned himself as a reformer, using his inaugural address to call for the South Sudanese people "to forgive, though we shall not forget" perceived injustices at the hands of the northern Sudanese over the preceding decades and announce a general amnesty for South Sudanese groups that had warred against the SPLM in the past. A few weeks later, he publicly addressed members of the military and police to warn them that rape, torture, and other human rights violations carried out by armed personnel would be considered criminal acts and prosecuted aggressively by the Ministry of Justice.
Kiir faced the first real crisis in his presidency of the Republic of South Sudan in early August 2011, when clashes over cattle erupted between Lou Nuer and Murle people in Jonglei and Warrap states, leaving over 600 dead. Kiir ordered the army to deploy to the unrest-hit areas to quell the violence, and the South Sudanese government claimed the next day that fighting had ended.
In mid-October 2011, Kiir announced South Sudan had applied for accession to the East African Community. He declared the EAC to be "at the centre of our hearts" due to its members' support of the South during the Sudanese civil wars.
On December 20, 2011 Kiir visited Israel to thank it for its support during the First Sudanese Civil War in 1956–1972, and met with Israeli president Shimon Peres to discuss establishing an embassy in Jerusalem, which would make South Sudan the only country to have one in that city.