It was only as late as 2014 that the Supreme Court of India, through National Legal Services Authority v. Union of India (NALSA Judgement), recognised the rights of transgender persons in India. However, despite this recognition and subsequent legislation by the parliament to protect the rights of transgender persons, the implementation of the same has been questionable. Moreover, a discussion regarding the rights of transgender persons vis-à-vis criminal justice institutions has been mostly absent. This chapter attempts to build on a report released by Commonwealth Human Rights (CHRI), which documented the number of transgender persons across Indian prisons while analysing the implementation of NALSA Judgement within prison settings. It also tries to analyse the subsequent developments that have taken place, such as an advisory by the Ministry of Home Affairs for the treatment of transgender prisoners in 2021, which is the first legal instrument on the basis of which transgender prisoners will be treated henceforth.