Robyn Browne, 23, was found dead at her flat in Marylebone, central London, in February 1997. She had been stabbed.
James Hopkins, of Leeds, was arrested in the city on Wednesday and was transferred to a London police station.
Mr Hopkins will appear at West London Magistrates' Court on Friday. Police said they had reviewed evidence using new techniques not available in 1997.
The victim, who was born James Errol Browne, was undergoing sex change treatment at the time of her death.
Ms Browne, of Gosfield Street, worked in London's West End.
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