Tariq Ramadan vehemently denies the allegations.
Henda Ayari, 40, who heads the women's organisation Les Libératrices, filed a complaint on Friday with prosecutors in the Rouen, France, alleging rape, sexual violence, harassment and intimidation by Ramadan, who is a professor of contemporary Islamic studies at Oxford.
In 2004, he was due to take up a post as professor of Islamic studies at the University of Notre Dame, in IN, but was barred entry by the American government, for "providing material support to a terrorist organisation".
Ayari's lawyer, Jonas Haddad, said she had not previously reported the alleged attack in 2012 out of fear.
Professor Ramadan is the grandson of the founder of the controversial Muslim brotherhood and was chosen by Tony Blair to work on a task force to help tackle extremism in the United Kingdom following the July 7 attacks in London in 2005.
An Oxford University spokesman said: "We are aware of the reports". The Liberators Association, of which Ayari is president, said on Facebook that she was "a victim of something very serious several years ago", but did not reveal the name of her aggressor for safety reasons.
In his book I chose freedom published in November of 2016 Flammarion, she described this man under the name of Zoubeyr, setting an appointment in his hotel room in Paris where this muslim scholar came to give a lecture. "It's enough to know that he profited from my weakness", Ayari wrote in her book.
"I confirm today the famous Zoubeyr is definitely Tariq Ramadan", Ayari wrote on Facebook.
"When I fought back and shouted at him to stop, he insulted me and humiliated me", she wrote.
"After revelations over the past few days of rape and sexual assault claims in the media, Henda has made a decision to say what happened to her and take legal action", said Jonas Haddad, Ayari's lawyer, according to The Guardian.
Haddad said he had filed the legal complaint against Ramadan with the prosecutor's office in Rouen, the city north of Paris where his client lives.