KontraS Aceh was founded on July 21, 1998, the founders consisted of various professional backgrounds, namely advocates, academics, journalists, students and NGO activists. At the time of its formation, KontraS Aceh was a branch of KontraS in Jakarta. In 2004, KontraS underwent a reorganization and became the KontraS Association, where KontraS Aceh as a regional KontraS became autonomous under the coordination of the KontraS Federation based in Jakarta.

Initially, KontraS Aceh was formed to handle cases of missing persons (disappearances) that occurred during the implementation of the Military Operations Area (DOM) in Aceh in 1989-1998. However, due to the many cases of violence and human rights violations that occurred during the DOM and post-DOM periods, KontraS Aceh finally handled other cases, namely torture (torture) and extra-judicial killings. The handling of this case was caused not only by the many findings in the field but also by the many complaints from victims of human rights violations to the KontraS Aceh office.

KontraS Aceh also strengthens conflict victims and victims of human rights violations, by providing an understanding of their rights and how to obtain these rights. To that end, KontraS Aceh held victim meetings both at the KontraS Aceh office, the network office, and in the victims' villages. The meeting was filled with discussions and education on human rights.

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