In 2016, the Australia Federal Government called a formal public inquiry under the arrangement of a Royal Commission to investigate the care and custody arrangements of children under detention orders in the Northern Territory. The NT youth detention system has been shown to be over-reliant on segregation as a behavior management tool which has likely resulted in the abuse of children in their care. This paper examines literature on the use of segregation to explain the progressively degenerating behavior of the children in custody and the likely negative physical and psychological impacts to the children involved. The paper calls for the prohibition of segregation of children arguing that a paradigm shift in the youth detention system to a model employing non-institutional care with trauma informed practice needs to be made.