Mountbatten-Windsor was arrested on 19 February, his 66th birthday, on suspicion of misconduct in public office following allegations he shared sensitive information with Epstein during his time as the UK’s trade envoy.
He was later stripped by the King of both his right to be a prince and his dukedom.
The Freedom of the City of London tradition dates back to 1237 and originally allowed people to carry out their trade.
The Corporation said it does not have the power to remove the Freedom because it is not an honour or office but a property right protected under both domestic law and the European Convention on Human Rights.
The court said officers had been instructed to begin proceedings to enable it to “lawfully remove the Freedom of the City” from the former royal.
Andrew inherited the Freedom of the City of London by patrimony, as the child of Prince Philip, the late Duke of Edinburgh, who was awarded it in 1948.