Jonglei state comprises nine counties: Bor, Akobo, Ayod, Uror, Duk, Nyirol, Pigi, Twic East, and Fangak.

[3] In the 21st century, Jonglei State has been marred by ethnic clashes, which the UNMISS estimated in May 2012 had affected the lives of over 140,000 people, and which have been magnified by the broader South Sudanese conflict since December 2013.

This school produced the first indigenous Anglican bishop to be consecrated in Dinka land, Daniel Deng Atong, the first person to be baptized in 1916 in Bor.

In 1912, the British established Pibor Post, a colonial era outpost which was originally called Fort Bruce in the eastern part of Jonglei State.

The First Sudanese Civil War which lasted from 1955 until 1972 broke out with a Southern rebellion in Torit in imatong state) against Northern armed officers.

[9] Much of the conflict is over basic resources of food, land, and water,[9] and personal grudges related to the abduction of women and children and theft of cattle.

[10] In November and December 2007, clashes between Murle and Dinke tribesmen had worsened to revenge attacks, killing over 34 people and injuring over 100.

[11] On one outbreak in late November 2007, eight Dinka tribesmen and 7,000 cattle were stole near the village of Padak, about 20 kilometres north-east of Bor.

The Geneva Small Arms Survey concluded that the "Murle–Lou Nuer conflict in Jonglei State is indicative of how tribal and political dynamics are intertwined in the post-CPA period.

"[12] A civilian disarmament operation targeting primarily the Nuer communities in 2005–06 resulted in a major outbreak of violence against the authorities, who believed that the crackdown was politically motivated.

[19] The Sudan People's Liberation Army (SPLA), international defence forces, and UN Peacekeepers are struggling to defuse the ongoing conflict and protect civilians against raids.

[19] A day later, a car traveling from Juba to Bor belonging to the South Sudan Ministry of Roads and Bridges was attacked near Panwell village in Bangachorot, killing the driver and wounding two policemen.

[21] On 9 April 2013, five Indian UNMISS troops and seven civilian UN employees (two UN staff and five contractors) were killed in a rebel ambush[22] in Jonglei while escorting a UN convoy between Pibor and Bor.

[25] A UN spokesman said that the fierce resistance put up by their peacekeepers forced the rebels to withdraw and saved the lives of many of the civilians.

[24] UN Secretary-General Ban Ki-moon labelled the killings a war crime, and called for the perpetrators to be brought to justice.

[30] It is "home to one of the largest migrations in the world with an estimated 800,000 white-eared kob antelope, 250,000 Mongalla gazelle and some 160,000 tiang moving across Jonglei State", according to the Wildlife Conservation Society.

The project was a highly controversial one, and in 1979 the Wildlife Clubs of South Sudan (WCSS) was established, which led the campaign against its construction.

Access to adequate healthcare in the state is extremely poor, and the situation has worsened since 2009 when Médecins Sans Frontières Belgium, who had been running the Bor Hospital, pulled out of the country amidst security concerns.