Transitional justice (TJ) is an ever-growing field, relevant all over the world. Indonesia has undergone a profound transition to democracy since the fall of Soeharto in 1998. However, separatist challenges have continuously tested the government’s ability to reform and account for past gross violations of human rights. This thesis explores the potential for TJ mechanisms in Papua as part of a wider peace dialogue. It also discusses the TJ mechanisms of prosecutions, truth commission, victim reparations and institutional reform. More importantly, the author applies these concepts to Indonesia in order to understand to what extent TJ mechanisms have been implemented during the past decade of transition. The thesis also examines the provincial conflict in Aceh and attempts to find lessons to be learned from the Indonesian government’s implementation of TJ mechanisms in resolving the conflict and in the post-conflict environment. Finally, the thesis culminates in an attempt to create a “blueprint” of similar mechanisms in Papua. Papua’s history is riddled with allegations of human rights violations and the situation remains a domestic failure of the reformasi. The author suggests that TJ mechanisms should play a role within a Papua-Jakarta dialogue.