Samuel Armstrong, 24, is alleged to have attacked the woman, who was working for him as an intern, after drinking with her in the Palace of Westminster.
The South Thanet MP’s aide is said to have taken advantage of his victim, who is in her twenties, when she fell asleep.
The court heard that the pair had been drinking in the Sports and Social Bar within the Houses of Parliament with two other people.
Later in the night, Mr Armstrong and the woman then went to Mr Mackinlay’s office, in the Norman Shaw building, where he played jazz music on a laptop.
They sat and talked on a three-seater sofa, where she fell asleep, jurors heard. He then began kissing and touching the woman before asking her back to his flat.
But when she said “no” several times, Mr Armstrong repeatedly called her a “bitch” before taking off her clothes and assaulting her.
Prosecutor Mark Heywood QC said the woman asked: “What are you doing?” To which Mr Armstrong allegedly replied: “This is what you want.”
Mr Heywood said he raped her twice, adding: “In doing so, he abused his role and his position.
“She, in distress, walked and ran through the corridors of Westminster, eventually finding and telling cleaning staff what had happened.
“He went out another way, using his pass and sending her messages, one of which suggested that he was concerned and that she contact him if she had ‘any issues’.”
Mr Armstrong, from Danbury in Essex, denies two counts of rape, one of sexual assault and one of assault by penetration on October 14 last year.
The court heard that the woman suffered a number of bruises and abrasions to her genitals, arms and mouth, which were consistent with, but do not prove, the allegations.
Mr Armstrong worked as a volunteer activist for the Conservative Party while at university before joining Mr Mackinlay’s staff when he was elected in 2015.
He was arrested at 5.39am on October 14 2016. In a statement to the police, he claimed what happened took place with “full consent.”
The trial, which is expected to take two weeks, continues.