Joseph Kony's arrival at the Ri kwangba camp, 500m north of the border with Congo, was announced on Sunday by Martin Ojul, the head of LRA's negotiating team in Sudan.
Kony, like his deputy, Vincent Otti, who has also arrived at the camp, is wanted by the International Criminal Court in the Hague on charges of war crimes and crimes against humanity.
The LRA signed a truce with the government last month after staging a violent insurgency for nearly 20 years that has killed thousands in the region encompassing northern Uganda, eastern Congo and southern Sudan.
Under the terms of the deal, the rebels are to gather in a series of camps in largely uninhabited areas of southern Sudan where they will be protected until a broader peace deal has been negotiated.
Another member of the LRA's negotiating team, Sunday Ocaya, said that about 3,500 fighters and 400 women and children had now arrived at the camps.
The fighters have until Tuesday to assemble at the camps.
Otti and Kony had implied that the deal could be under threat because they were unwilling to emerge from the jungle with the threat of ICC charges hanging over their heads.
However, the Ugandan president has offered the two men an amnesty in return for an end to the insurgency.
Yoweri Museveni has come under criticism from human rights groups for his offer, but argues that peace is currently a more pressing objective than a prolonged international trial.
UN officials estimate that the LRA has kidnapped about 20,000 children in the past two decades, forcing the boys to become soldiers and the girls sex slaves.
Otti told UN officials on September 11 that the group would be willing to hand over women and children.
The rebels were known for cutting off the tongues and lips of civilians during the insurgency.
The LRA formed from the remnants of a northern Uganda rebellion that began in 1986 after Museveni, a southerner, overthrew a military government.