The article examines how to address the report of the African Union Commission of Inquiry on South Sudan, which accuses the Government of South Sudan and the rebels of committing “crimes against humanity” and violating “international humanitarian law” in the war of December 2013. The Commission recommends “an Africa-led, Africa-owned, Africa-resourced legal mechanism, under the aegis of the African Union and with support from the United Nations, to bring those with the greatest responsibility at the highest level to accountability” in a court. Second, the Agreement on the Resolution of the Conflict in the Republic of South Sudan asked for establishing a hybrid court in South Sudan to investigate and prosecute the perpetrators of “genocide, crimes against humanity and war crimes”. The Cabinet of South Sudan approved, in its resolution on 29 January 2021, the establishment of the court. On the other hand, the Government of South Sudan rejected accountability for the perpetrators of international crimes in its resolution at the Transition Justice Conference and recommended “amnesty” for those admitting the commission of international crimes in Juba, Malakal, Bor and Bentiu. The research findings show that amnesty threatens peace and security because customary law rejects amnesty. Its implementation generates systematic vengeance from the clan of those killed. The research recommends the establishment of a hybrid court that adopts the complementarity principle in compatibility with the African customary law of blood compensation. The authoritative national criminal courts in South Sudan omit capital punishment on the grounds that (a) killer(s) pay(s) blood compensation, apok or cot, to the survivors of (a) killed person(s) with 51 cattle. The payment changes the penalties of life imprisonment, which international criminal law imposes on the perpetrators of international crimes and the death penalty, which African criminal law imposes on the confirmed killer(s). Finally, the tribunal imposes 10-year terms of imprisonment on the confirmed perpetrators of international crimes.