Egeland held talks with the Lord's Resistance Army leader, Joseph Kony, in a jungle clearing in southern Sudan in a bid to help free women and children enslaved by the cult-like group during their 20-year conflict with the Ugandan government.
They exchanged a brief, formal handshake before holding talks under a green, U.N. erected tent.
He is the first high-ranking U.N. official to meet Kony, who has declared himself a Christian prophet fighting to rule Uganda and its 26 million people by the Ten Commandments.
The infamous rebel leader kept Egeland waiting for two hours at the makeshift camp close to the border with Congo.
Kony has only appeared in public a handful of times, fearing arrest and extradition to the Hague to answer war crimes charges. During the LRA's two-decade insurgency, the group has been blamed for murder, mutilations and kidnapping children for use as soldiers and sex slaves.
Almost 2 million people have been displaced by the conflict, aid organizations say.
Egeland traveled by helicopter to Ri-Kwangba, a neutral zone 1,600 feet north of the Congo border where the rebels are to gather under the terms of a peace deal with the Ugandan government. He was accompanied by Riek Machar, vice president of southern Sudan and chief mediator in peace talks, a team of U.N. security officials and Ugandan government and rebel negotiators.
He also met with Vincent Otti, the LRA deputy who is also wanted for war crimes.
Security was extremely tight. Around 100 LRA fighters loitered on the outskirts of the clearing.
"I am a humanitarian worker, I help people by relating to people who can unlock situations," Egeland told journalists late Saturday before his party officially announced the visit.
Last year, the Netherlands-based International Criminal Court issued arrest warrants for Kony, Otti and three other LRA commanders on numerous charges of war crimes and crimes against humanity.
Egeland said he was unwilling to discuss the issue of the arrest warrants, which the rebels say threaten the fragile peace deal signed with the government in southern Sudan's capital, Juba.
The rebels want the warrants dropped before they sign a comprehensive peace deal, while the Ugandan government says it will ask for them to be lifted only after a full agreement is reached.
Uganda's government welcomed Egeland's meeting with Kony.
"If he can secure the release of women and children through his meeting then that would be a very positive boost for the Juba talks," Ruhakana Rugunda, head of the government negotiating team and Uganda's minister of internal affairs, said late Saturday.
Under the terms of the August truce, rebel fighters were to gather in September at two neutral points. However the deal has been undermined with both sides trading accusations of hostility. Earlier this month they agreed an extension to the truce as they try to thrash out a full deal.
The Lord's Resistance Army is made up of the remnants of a rebellion that began after Ugandan President Yoweri Museveni took power in 1986.
Its political agenda is unclear. But it has set up rear bases in Sudan and Congo, and has been accused of attacking civilians and threatening stability in those countries.
The conflict has spilled over into southern Sudan and Congo, causing further instability in the volatile region. If both sides reach a comprehensive deal, it will be a major breakthrough in pacifying northern Uganda, eastern Congo and southern Sudan.
Rebels from all three nations operated across the borders with impunity for decades until a peace accord halted Congo's civil war in 2003 and southern Sudanese rebels joined Sudan's government in 2005.
After his two-day visit to Juba, Egeland will fly on to the troubled Darfur region in Sudan's west. The trip will be his last to Africa as the United Nations under-secretary-general for humanitarian affairs and emergency relief coordinator. He steps down next month.