The Boko Haram conflict in Nigeria has caused a lot of deaths, mass abductions and gross human rights abuses resulting in the dislocation of several families as refugees in neighbouring countries. Other victims have been rendered homeless and destitute as internally displaced persons. The Nigerian government’s response has not been very effective fuelling the suspicion that the insurgency is a combination Islamic militancy and political competition for power. It does not seem that the solution to the Boko Haram conflict is military engagement as other conflicts have shown. This article uses the Nigerian experience between the Niger Delta militants and the Boko Haram insurgency as a case study to discuss the difficult choices between peace, justice and reconciliation. It focuses on the activities of international justice institutions, provisions of the Rome Statute of the International Criminal Court, and the debate between amnesty, prosecution and the interests of justice. The article argues that the emergence of Boko Haram as a terrorist group in Nigeria affiliated with other international terrorist groups has raised the stakes. The involvement of the Court in the conflict is also very significant as it is not bound by any amnesty or reconciliation programme that could be reached between the Nigerian government and Boko Haram members.