Thereafter, he worked as the special officer, Vigilance Cell, Madras High Court.
He was then further elevated as the Chief Justice of the Orissa High Court and sworn in on 27 February 2013.
He was appointed a judge of The Supreme Court of India and sworn in on 19 September 2013.
Nagappan who held a relatively short tenure retired as a Judge of the Supreme Court of India on 3 October 2016.
A three judge bench of the Supreme Court, comprising Nagappan, Jasti Chelameswar, and Sharad Arvind Bobde ratified an earlier order of the Supreme Court and clarified that no Indian citizen without an Aadhaar card can be deprived of basic services and government subsidies.