Andrea Leadsom knew of a rape case that had been reported to the Commons, the Victoria Derbyshire show understands.
The Commons leader has been accused by the alleged victim, an ex-Tory activist, of ignoring concerns over the "toxic" culture of Westminster.
"Amanda" said she told the Commons clerk she had been raped by someone who worked for a Conservative MP.
The BBC has established Ms Leadsom was told about the alleged case by the clerk in a regular briefing.
Ms Leadsom's office initially said she did not receive an official complaint in relation to the alleged rape.
Both the clerk and Ms Leadsom said it would not have been appropriate to take any further action given the ongoing criminal case at the time.
The alleged rape did not take place inside Parliament.
Amanda - whose name has been changed to protect the identity of both parties - says she was raped "by someone senior to me in the Conservative Party.
"It was violent. It wasn't in Westminster, it was in my own home."
"And it shouldn't have happened. I remember the attack, during the attack. I remember the room disappearing around me and thinking I was going to die.
"When he left the next day I was at the police station within an hour and I reported it."
As she waited for a trial date, she decided to tell the Commons officials about the alleged rape. She explained how she felt the "heavy-drinking and sex-driven" culture within Westminster had contributed to it.
This programme has confirmed Amanda had a 25-minute conversation with the House of Commons clerk, David Natzler.
She said she left the conversation believing her concerns about both the culture and her alleged attack would be passed on to the then-Chief Whip Gavin Williamson and the Leader of the House, Andrea Leadsom - and that a meeting might follow.
Mr Williamson has just been promoted to defence secretary after Michael Fallon resigned over his "general conduct" and Mrs Leadsom has since said Parliament would take a "zero-tolerance" approach to allegations of sexual misconduct.
But Amanda said: "I never received contact from either of them. The parliamentary authorities never followed it up with me either. I heard nothing."
The clerk refused to confirm who he spoke to about what he had been told, saying that Amanda's concerns were "informally reported onwards" and were "acted on".
The BBC understands the allegation and Amanda's general concerns were raised by the clerk at a regular meeting with Ms Leadsom.
But no-one will say how exactly it was acted upon and Amanda was not told either.
It is understood Mr Williamson insists none of the claims was passed on to him.
Amanda said the incident had "destroyed" her.
"I question how I could be so stupid as to get into that political scene," she added. "And I blame myself for doing so because it led to what happened to me. If I hadn't have got into that scene I wouldn't have been attacked. It's as simple as that."
She added it had made her feel "worthless and as if my experience wasn't important and that the experiences of others who had who had had similar things happen to them weren't important either".
The man Amanda had accused of rape, who was not an MP, strongly denied the allegation and the case was later dropped after a review of the evidence.
But at the time she told the parliamentary authorities about it and her general concerns the case was due to go to trial and she says she was ignored despite their seriousness.
In a statement, the clerk confirmed the conversation took place.
It added: "The allegation was mentioned but was not the focus of the discussion, as the incident had not taken place on the Parliamentary Estate, and the activist had not been employed on the estate.
"There was no question of formally 'referring' the allegations to other House authorities as there was already a criminal case under way."
Amanda said the clerk took her concerns extremely seriously.
Watch the Victoria Derbyshire programme on weekdays between 09:00 and 11:00 on BBC Two and the BBC News Channel.