Gary Dobbie told the 15-year-old girl that she had "beard rash", indicating he knew what had happened, jurors were told on Thursday.
Dobbie, head of house at Christ's Hospital School in the 1990s, was allegedly told about the encounter by history teacher James Husband,
Husband told the pupil "It's OK, I've had a vasectomy" before raping her, the court heard.
The victim reported Husband to the Horsham school's chaplain but no action was taken. Even her mother did not believe her story, Hove Crown Court heard.
Years of alleged abuse
The pair, who both worked at the prestigious West Sussex school and lived in the grounds, are standing trial after denying sexually abusing eight pupils over the course of 13 years.
Dobbie, aged 66, was teaching at Shrewsbury School at the time of his arrest in 2016.
Eloise Marshall, prosecuting, told the court victims believed the teachers would "laugh" together about their exploits.
Husband, 68, of Wigginton in York, denies four counts of rape and five of indecently assaulting a girl as young as 14 between 1990 and 1994. He claims they had "consensual sex" once when she was 16.
He left the school after it emerged he was having a consensual affair with a different pupil who was not underage and not a complainant in the case, Ms Marshall said.
The girl's diary entries suggested they had sex in Husband's study - which is where he is accused of abusing his alleged victim, the court heard.
Dobbie, of Albi in France and formerly of Hereford, faces a string of allegations against six boys and two girls as young as 12 between 1998 and 2001.
He denies 12 counts of indecently assaulting four boys and two girls, attempting to indecently assault a boy and two counts of indecency with a child.
Ms Marshall said: "Both the men knew each other and there is some evidence to suggest that they discussed what they were doing."
Husband's alleged victim "lay there like a rag doll" while he raped her and waited for it to be over, the court heard.
It became so frequent she began to "hate" what was happening, was "disgusted with herself" and was suicidal, Ms Marshall said.
Dobbie "groomed" pupils, by hosting dinner parties at his house in the school grounds with "favourite" students, jurors were told. He would allegedly ply them with whisky and wine while talk about their sexual encounters was "encouraged".
At one of the gatherings an alleged victim recalls a man who also attended as a guest rating the boys in order of their attractiveness, to Dobbie's "delight", Ms Marshall said.
On another occasion after giving a girl alcohol, she came out of the bathroom to find Dobbie had undone his trousers and was "grinning at her", the court heard. Fearing he wanted to have sex, she left the property.
She told her mother after she moved on from the school who phoned housemaster Neil Flemming but no action was taken, Ms Marshall said.
When questioned by police, Dobbie branded the claims "totally untrue".
The trial heard how he took a boy as young as 12 to a bedroom and told him to take off his breeches and underwear while Dobbie performed a sex act on himself.
Another recalls falling asleep on Dobbie's sofa and waking up to find him kneeling beside him with his hand in his shirt, Ms Marshall said.
The teacher even helped raise money for another pupil - allegedly abused over a period of six years - to take a gap year after leaving school but assaulted him when he returned for a visit, the court heard.
Founded in the 16th century, Christ's Hospital charges boarders up to £31,500 a year and counts Sir Barnes Wallis, inventor of the bouncing bomb, and poet Samuel Taylor Coleridge as alumni.
Pupils still wear a Tudor-style uniform consisting of a long blue coat and high yellow socks.
The trial, expected to last six weeks, continues.