But the brief meeting, hoped to boost peace talks to end northern Uganda's brutal, two-decade war, ended inconclusively, with Kony griping about Kampala and war crimes charges and denying the rebels hold captives, officials said.
Despite that, Mr Egeland said he thought it had been "an important meeting because it was the first time we have been able to impress on the highest command of the LRA the whole range of humanitarian issues."
Mr Egeland and Kony, who arrived two hours late, shook hands at a remote jungle clearing at the neutral camp of Ri-Rwangba on the border between southern Sudan and the Democratic Republic of Congo, where the top rebel leadership is based.
The elusive rebel supremo, who emerged from the bush on foot with heavily armed guards, then met Mr Egeland under a green UN tent in what is believed to be the shadowy guerrilla leader's highest-level international contact ever.
After the 10-minute meeting, Kony, clad in civilian garb with sunglasses, a cap and a green shirt, said the LRA was holding no one against their will, adding: "We don't have any children or wounded, only combatants."
On his arrival at the heavily guarded site, where he first met Kony's number two Vincent Otti for 40 minutes, Mr Egeland said he wanted "to talk about women, children and (the) sick" allegedly held by the LRA.
"I asked what I should tell the mothers who have been crying and begging to see their abducted children," he told reporters afterwards.
But LRA officials at the meeting said Kony told Mr Egeland the only women and children they had were fighters' wives and offspring who would not be split up.
"Taking them away would be equivalent to breaking up families," LRA spokesman Godfrey Ayoo told news agency AFP.
He said Kony had also complained to Mr Egeland about Ugandan violations of a landmark truce signed in August and renewed last month.
"They are using helicopter gunships to attack our troops," Mr Ayoo said, maintaining the Ugandan military had killed four people, including a mother and child, on Saturday in a raid in southern Sudan.
The peace talks in Juba, the capital of autonomous south Sudan, have stalled since the signing of the truce, as the two sides trade accusations of violations.
Under the truce, the rebels were gathering at two neutral camps in south Sudan, of which Ri-Kwangba is one, but have left, alleging the Ugandan army plans to attack them there.
Kony, who rarely appears in public, reiterated to Mr Egeland the LRA's insistence they will not return "as long as (Ugandan) soldiers are still in southern Sudan," said Mr Ayoo.
A self-described prophet who claims to speak directly to God, Kony has led the LRA in a 19-year insurgency aimed at replacing the Kampala government with one based on the Biblical Ten Commandments.
He, Otti and three other rebels have been charged by the International
Criminal Court for atrocities allegedly committed since they took leadership of a rebellion by northern Uganda's ethnic Acholi minority in 1988.
They deny the allegations and claim any such abuses were committed by the Ugandan military, but hundreds of witnesses accuse the rebels of large-scale massacres, rapes, mutilations and mass abductions.
Mr Ayoo said Kony had told Mr Egeland "the biggest obstacle to the search of peace in northern Uganda was the ICC arrest warrants," on which the talks have stumbled since they began in July.
"He appealed to Egeland to intervene and have the warrants withdrawn in order to save the peace process," Mr Ayoo said.
Mr Egeland said before the meeting he would raise only humanitarian issues and would not discuss the ICC, an independent organisation.
After seeing Kony, he told reporters in Juba that he had made clear to the rebels that "peace and justice has to go hand-in-hand."
"There can be no lasting peace without justice," Mr Egeland said.
Mr Otti said neither he nor Kony would attend the talks until they are quashed, fearing arrest. "If the warrants are lifted, then we can go to the peace talks," Otti said.
Uganda has promised total amnesty to the rebels if they sign a peace deal and agree to go through traditional reconciliation processes, but has ruled out asking The Hague-based court to quash the charges until they do so.
The conflict in northern Uganda has claimed tens of thousands of lives and displaced nearly two million people, and is regularly described as one of the world's worst, and most-forgotten, humanitarian crises by Mr Egeland and others.