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Pope Francis on Saturday will meet victims of South Sudan's civil war, a day after delivering an impassioned plea for the country's leaders to recommit to peace for the sake of their long-suffering people.

Francis is making the first papal visit to South Sudan since it gained independence from Sudan in 2011 and then plunged into a brutal ethnic conflict that left the young nation divided and traumatised.

Some 380,000 people died in five years of bloodshed before the civil war formally ended in 2018, with a ceasefire between warring leaders who remain in power today.

But the country remains fragile and violent, and Francis, who tried to broker peace between the rival parties, is visiting South Sudan as it lurches from one crisis to the next.

At his first event on Saturday, the wheelchair-bound pope met South Sudan's religious leaders, who work with the poor and marginalised and are deeply respected in the devout country where 60 percent of its 12 million people are Christian.

He said they must "step into the middle of [people's] sufferings and tears", adding that the Church had a duty to be "willing to dirty its hands for people".

Several thousand turned out early to wait for the 86-year-old pontiff in the courtyard of the Cathedral of Saint Therese, many waving national flags and ululating as they gave him a jubilant welcome.

"We came here to receive his blessings. This is all about peace. Pope Francis is not even walking, and he is still coming here to encourage our leaders," said John Makuei, 24.

He said he arrived before dawn, so he did not miss this "historic day".

"I am so so happy," said 36-year-old Adongpiny Harriet, wiping away sweat after she joined an impromptu dance outside the cathedral following the pope's blessing.

"It is the first time to see papa in my country. I feel so privileged."

'A new start'

Later on Saturday, the Argentine pontiff will address a group of South Sudanese living in a camp outside Juba who were forced to flee ethnic violence during the war.

They will be brought to the capital for an audience with Francis, who has made the defence of migrants and those on the margins a pillar of his papacy.

Despite a peace deal technically ending the war, conflict still drives people from their homes, and there are some 2.2 million internally displaced people across South Sudan, according to UN data from December.

On Saturday evening, Francis will hold a joint prayer with the Archbishop of Canterbury and the Moderator of the General Assembly of the Church of Scotland, who joined him in the country.

On Friday, Francis delivered a pointed speech to the country's political leaders, warning they must make "a new start" toward reconciliation and end the greed and power struggles tearing the nation apart.

"Future generations will either venerate your names or cancel their memory, based on what you now do," he told an audience that included President Salva Kiir and his rival and deputy Riek Machar, as well as diplomats, religious leaders and traditional kings.

"No more bloodshed, no more conflicts, no more violence and mutual recriminations about who is responsible for it, no more leaving your people athirst for peace."

Prisoners pardoned

The pope promised in 2019 to travel to South Sudan, when he hosted Kiir and Machar at a Vatican retreat and asked them to respect a hard-fought ceasefire for their people.

In scenes that reverberated in South Sudan, Francis knelt and kissed the feet of two foes whose personal armies had been accused of horrific war crimes.

But four years later, the country remains mired in intractable conflict and lags at the bottom of global rankings on health, poverty and stable governance.

Human rights groups have urged Francis to press South Sudan's leaders to address widespread impunity for abuses and deliver justice for victims of war-era atrocities committed on their watch.

Workneh Gebeyehu, secretary general of the regional grouping IGAD also called in a statement on Twitter on the leaders and people of South Sudan to "heed his call for durable peace & stability".

After his meeting with the pope, Kiir announced in a decree he was pardoning 71 prisoners, including 36 on death row, but gave no other details.

The pope's stop in South Sudan follows a visit to the Democratic Republic of Congo, another resource-rich country plagued by persistent conflict and also often overlooked by the world.

The visit – Francis's fifth to Africa – was initially scheduled for 2022 but had to be postponed because of problems with the pope's knee.

The affliction has made him dependent on a wheelchair and has seen the itinerary pared back in both countries.