The girl, aged 15 at the time, was a "frequent runaway" and had met a man called David Ayrton on the day of the attack more than 10 years ago.
The 34-year-old, now called Davina, denies raping the teenager in a garage in Portsmouth in the autumn of 2004.
Portsmouth Crown Court was told the alleged incident happened while two others were asleep in the garage.
The teenager, who cannot be identified, stayed there when hiding from her parents.
She told the court although she had shouted and sworn at the defendant to stop the attack, her friend and her boyfriend had not woken up.
She added that she had "only drunk a can and a half of Foster's" and had a clear recollection of the events.
The friend who was with her in the garage at the time told the court the alleged victim was a "vulnerable" girl at the time.
She said she was eventually woken up by the teenager who was "screaming and crying and asking for help".
The person alleged to be Ms Ayrton was then "ejected" from the garage by the girl's boyfriend.
The court heard the victim made a complaint to police in December 2004 but had not assisted officers because she was "anti-police" at the time.
Chris Stopa, prosecuting, said Ms Ayrton has learning difficulties and told a worker at the care home in Fordingbridge where she lives about the incident in 2014.
Police then contacted the alleged victim, leading to the prosecution.
Ms Ayrton denies one charge of rape between October and November 2004.
The trial continues.
A teenage girl was raped in a garage by a transgender woman when she was still living as a man, a court has heard.