A former student at St. Paul’s School has accused the elite boarding school in Concord, N.H., of failing to protect her from sexual assault when she was a freshman in the 2012-2013 school year, according to a new federal lawsuit.

The lawsuit was filed Friday in US District Court in Concord, N.H., on behalf of the student, who lives in Maryland. She alleges the tony Episcopal school — which has educated Kennedys, Astors, and Vanderbilts — failed to protect her under Title IX, the federal law that prohibits sex discrimination in education.

The student is identified only as Jane Doe in the complaint, which alleges that a classmate she dated forced her to perform sex acts against her will and that other boys groped her without consent.

In a letter to the St. Paul’s community on Friday, the president of the school’s board of trustees, Archibald Cox Jr., said officials “take these allegations very seriously.’’

“We are learning about these allegations for the first time this evening as we were not contacted before the complaint was filed,’’ wrote Cox, son of the famous Watergate prosecutor, also a St. Paul’s graduate.

He added that school officials “do not know whether they are accurate or not.’’

“In my experience this administration has taken all reporting obligations seriously and has fulfilled them,’’ Cox wrote.

St. Paul’s “hypersexualized culture’’ contributed to the student being harassed, according to the filing. It claims that the school’s leader, Michael G. Hirschfeld, was well aware of the school’s culture of “scoring’’ and that a male student had even sexually propositioned Hirschfeld’s wife.

Hirschfeld denied the allegations against him in a statement to the Globe on Saturday.

“I vehemently refute that I ever failed in my responsibility to report an alleged sexual assault to Concord Police. This statement is false,’’ he said. “I look forward to cooperating fully with any investigation into such claims.’’

Hirschfeld announced in January that he will step down at the end of the 2018-2019 school year.

The plaintiff’s attorney, Charles G. Douglas III, of Concord, N.H., could not be reached Saturday.

The lawsuit is the latest to be filed against the school, which has been heavily scrutinized for its response to multiple allegations of sexual misconduct.

In 2015, a former St. Paul’s student, Owen Labrie, was acquitted of raping a 15-year-old freshman, but he was found guilty on lesser sexual assault charges. He is requesting that the New Hampshire Supreme Court grant him a new trial.

Chessy Prout, Labrie’s accuser, who is now 19, has become a vocal advocate for victims of sexual assault and wrote a book about her experiences with Jenn Abelson, a Boston Globe reporter.

Prout’s parents filed a lawsuit in 2016 alleging that St. Paul’s fostered and condoned “a tradition of ritualized statutory rape.’’ The school announced in January that it had settled that suit.

Prout could not be reached for comment on Saturday because she was traveling back to the United States from a trip to Hong Kong and Japan, where she was continuing her advocacy work for victims of sexual assault.

Speaking by phone from Hong Kong, her father, Alex Prout, said he and his wife, Susan, support the victim identified as Jane Doe.

“We want to let Jane know that we believe her and we stand with her,’’ he said. “Having gone through it ourselves, we understand how isolating this can be for victims and their families, especially at St. Paul’s School, where there has been such a long history of silence. . . . These lawsuits emerge because the school continues to deny the existence of any issues.’’

According to the court filing, the plaintiff — who was just 13 when she began attending the school — was repeatedly sexually assaulted by a boy she dated, who forced her to perform oral sex on him against her will on at least five occasions and attempted to insert his fingers into her vagina without her consent.

She also was allegedly assaulted at school dances, where boys “grabbed and groped her, thrusted their bodies against her, and placed their hands down her pants while administrators stood by and did nothing,’’ according to the suit.

The “sexual assaults and harassment Ms. Doe suffered [are] a direct result of [the school’s] utter breach of its duty to protect children under its care and to provide an education free from sexual harassment and other forms of gender-based harassment,’’ the lawsuit states.

Leaders at St. Paul’s were told of the assaults but did not report them to police, as required by law, nor did they tell her parents, according to the filing. Instead, an administrator allegedly accused the victim of “making up a story about being raped’’ and of stealing from students who had richer families.

The student accuses St. Paul’s of negligence and “intentional infliction of emotional distress,’’ during her brief tenure at the school. She has experienced “nausea, vomiting, elevated heart rate, sweating, nightmares, night terrors, and inability to sleep’’ because of the trauma she experienced, according to the filing.

A recruiter for St. Paul’s had told the girl and her parents that “the school offered a caring, closely knit community in which she would have ‘180 parents’ looking out for her safety and well-being,’’ according to the suit.

But she was sexually targeted by older boys from “the moment she set foot on campus’’ and “experienced unwelcome sexual advances from some male students who were emboldened by formal and informal ‘traditions’ at the school,’’ the filing says.

Those traditions, according to the suit, include male students rating underage girls in their student directories by attractiveness and using those ratings in “games of sexual conquest.’’

The school’s so-called “senior salute’’ tradition, in which senior boys tried to have sex with as many younger girls as possible, and its culture of “scoring’’ by having sex with underage girls, were an open secret, acknowledged in the student newspaper and allegedly well known among faculty and administrators, according to the filing.

A state investigation into sexual assault allegations at the school led to the arrest in February of a former instructor, David O. Pook, 47, who allegedly conspired to hide a relationship with a female student.

New Hampshire’s attorney general launched that investigation last year after an inquiry by lawyers working for the prep school identified 13 former faculty and staff members who had engaged in sexual misconduct over four decades. A second investigation last fall identified an additional five faculty members suspected of improper conduct and another 15 victims.

Following Pook’s arrest, the school said it had fired him “after he violated school rules governing boundaries between faculty and students’’ but said it “found no evidence of a sexual relationship between Mr. Pook and a student.’’

In a separate case, two former students filed a lawsuit last week in a New Hampshire state court accusing former teachers of abuse, including late Massachusetts Congressman Gerry Studds.

Felicia Gans of the Globe staff contributed to this story. Jeremy C. Fox can be reached at jeremy.fox@globe.com. Kathy McCabe can be reached at katherine.mccabe @globe.com.