The Lord's Resistance Army (LRA), notorious for torture and ethnic cleansing of civilians, signed a truce with the government on Saturday which came into effect on Tuesday.
An army spokesman, Major Felix Kulaije, said on Tuesday: "The cessation of hostilities is in effect now and involves the Ugandan army halting their search-and-destroy operations."
The truce gives rebels three weeks to gather at two assembly points in largely uninhabited areas across the border in southern Sudan, where they will be protected and monitored.
Ruth Nankabirwa, Uganda's deputy defence minister, said: "We don't expect to hear any gunfire in these areas."
Chris Magezi, an army spokesman for northern Uganda, said that he did not expect a mass movement of rebel fighters right away. "The LRA do not have the confidence to move openly, so they will probably go secretively in groups on foot," he said.
If the deal holds, it will be a breakthrough in pacifying the African region that joins northern Uganda, eastern Congo and southern Sudan.
Armed groups from all three nations operated across borders with impunity for decades until a peace accord halted Congo's civil war in 2003 and southern Sudanese rebels joined Sudan's government last year.
Kony mixed northern politics
with religious mysticism
Peace would open northern Uganda to greater oil and mineral exploration and allow hundreds of thousands of refugees to return to their farms.
The LRA was formed from the remnants of a northern Uganda rebellion that began in 1986 after the president, Yoweri Museveni - a southerner, overthrew a brutal military junta.
Joseph Kony, leader of the LRA, mixed northern politics with religious mysticism, declaring himself a Christian prophet fighting to rule the country of 26 million people by the Ten Commandments.
UN officials estimate that Kony's fighters kidnapped about 20,000 children over the past 19 years, turning the boys into soldiers and the girls into sex slaves for rebel commanders.
Rebel attacks and atrocities also drove 1.7 million from their homes.
The International Criminal Court has issued arrest warrants for Kony and four other rebel leaders; but the Ugandan government has promised not to turn them over in return for an end to the insurgency.