The 58-year-old Swiss national has already been charged in France with raping four other women, which he denies.
A father of four, whose grandfather founded Egypt's Muslim Brotherhood, Ramadan was a professor of contemporary Islamic studies at the University of Oxford until he was forced to take leave when rape allegations surfaced in 2017.
The latest charge relates to the alleged rape in 2013 and 2014 of a former escort girl who was one of the first to accuse him of sexual assault.
Her testimony had forced Ramadan to admit to extramarital relations for the first time, but he stressed they were "consensual".
Paris prosecutors had asked him to be charged in this case in 2018 but judges had suspended their decision until now.
"There is no new element" in the probe, Ramadan's lawyers told the AFP news agency on Thursday after Ramadan was questioned and charged by the judges.
"It's not Tariq Ramadan's word against that of this woman, it is this woman against her own serious and consistent lies," they said.
The complainant's lawyer, however, said "the probe has shown how the word of my client was as reliable as it was constant".
Being charged in France does not necessarily mean a suspect will end up on trial, as a case can still be dropped for lack of evidence.
Ramadan was imprisoned in France in February 2018 after two rape allegations led to criminal investigations. A third allegation was later filed. A 2018 complaint by the Swiss woman – she accused Ramadan of raping her in a Geneva hotel in 2008 – has still not come to a conclusion in Switzerland. The scholar is also accused of having had inappropriate relations with students while teaching at a Geneva school.
Ramadan denies all allegations against him. He was released from prison in France last November after ten months. He has to report to a police station once every two weeks and is allowed to go to Switzerland for the Swiss case; he is due to travel to Geneva at the beginning of November.