The agreement sets out that Kony and his rebel commanders will be tried by a Ugandan court rather than by the International Criminal Court (ICC) in The Hague, a key factor that clinched the deal.
The ICC, which insists it will try Kony, indicted him in 2005 for war crimes and crimes against humanity.
The agreed between the government and the LRA is vague on disarmament and the release of the hundreds of children and women, still believed to be in LRA captivity.
Reik Machar, the Sudanese vice-president and chief mediator, confirmed that Kony would be in Sudan to sign the agreement.
"They [LRA] told me that he would be here." Machar said.
Twenty years of fighting have left thousands of Ugandans dead and displaced two million people, mainly in northern Uganda.
Several thousands have also been killed in southern Sudan where the LRA was once based.
A ceasefire was agreed in August 2006, paving the way for peace talks in Juba, Sudan, that dragged on for more than a year and a half.
However, even with an agreement, Kony is not expected to return to the capital Kampala.