This paper aims at identifying the roles and functions of amnesty in transitional justice with reference to the prosecution proceedings at International Criminal Court (ICC). First, it gives an overview of the evolution of the notion of transitional justice and the role of amnesty in the international society. It points out that the measures of amnesty in transitional justice have conflicting roles: to facilitate the establishment of the new society on the one hand and to impede the accountability of perpetrators by forgoing past human rights’ abuses on the other. It then analyzes the conceptual changes of amnesty from positive to negative terms; historically it served to establish a better relationship between enemies by forgoing past events or to liberate persons detained for political reasons. It turned out that measures or laws of amnesty were abused by political leaders for the purpose of exempting themselves from being charged in the transitional period. This generated the idea that amnesty should be abolished at the international society. The United Nations commissioned a study on amnesty which proposed the restriction on the application of amnesty. Second, the paper studies the prosecution policy of ICC, clarifying the policy of respecting and strengthening national sovereignty and the principle of complementarity. Third, the paper examines how the ICC addresses the domestic measures of amnesty in its prosecution procedures by scrutinizing the cases of Uganda and Sudan. The two cases demonstrate that amnesty measures taken by governments are not so much for justice seeking or reconciliation but as for a political avoidance of the prosecution procedure before the ICC. In addition, they further indicate the tendency of ICC to adopt a positive prosecution policy by admitting and exercising its jurisdiction actively. Whereas this assists in strengthening the rule of law at the international level, it may hinder the capacity building of domestic jurisdiction as states make use of the ICC procedures as an alternative to their own judiciary, regardless of ICC’s complementary function. The paper concludes that while the amnesty measures have been employed for justice seeking by nation states, the efforts by ICC to pursue its judicial function in stricto sensu have caused some dilemmas regarding whose justice should be sought and how. The paper finds that the ICC, while recognizing its principle of complementarity that presumes and supports national sovereignty, does fortify its mandate by positively affirming its jurisdiction.