Vicky Thompson, 21, was being held at Armley, Leeds, where she was pronounced dead on Friday.
Friends of Thompson, who was born male but had identified as female since her mid-teens, said she had asked to be sent to a female prison.
An investigation into her death has been launched, the Prison Service said.
Thompson, from Keighley, West Yorkshire, was handed a 12-month jail term in August which was suspended for 24 months.
The BBC understands she later breached the terms of the sentence, and was remanded in custody at Bradford Crown Court.
Her solicitor, Mohammed Hussain, said he had advised the judge she was "essentially a woman" and asked for her to be sent to New Hall women's prison, near Wakefield.
He said he also asked for any sentence to be reduced if it was decided Thompson would be sent to an all-male prison.
Mr Hussain described Thompson, who had not undergone gender reassignment surgery, as a vulnerable transgender person.
Alex Kaye, from SafeT, which represents transgender people, said he hoped Ms Thompson's death would bring about a change in the law.
"Any woman would not be happy to be in a male prison regardless of any gender identity history," he said.