Olympic gold-medal-winning gymnast McKayla Maroney signed a confidential $1.25 million settlement agreement with USA Gymnastics in December 2016 to resolve claims related to her alleged yearslong sexual abuse by the national team’s longtime doctor, Larry Nassar.

The existence of the settlement, the terms of which were described to The Wall Street Journal by a person familiar with the settlement, was revealed in a lawsuit filed by Maroney Wednesday in Los Angeles Superior Court, seeking damages from the U.S. Olympic Committee and Michigan State University, where Nassar worked for decades, on the grounds of negligence, sexual harassment and other civil claims.

The lawsuit also names USA Gymnastics as a defendant and seeks to invalidate parts of Maroney’s settlement, claiming the agreement’s nondisclosure and non-disparagement clauses are illegal.

The lawsuit, brought by one of the most celebrated and recognizable Olympians of the modern era, casts a harsh light on the U.S. Olympic leadership, alleging that officials put a premium on secrecy that came at the expense of athletes. And the settlement brings into sharp relief the potential exposure USA Gymnastics faces, placing a price tag on abuse that could reshape the embattled governing body as it strives to recover from the scandal.

It isn’t known if USA Gymnastics paid settlements to any other alleged victims of Nassar, who has been accused by scores of girls and women—including two of Maroney’s former Olympic teammates—of sexually abusing them under the pretense of providing medical care. Nassar pleaded guilty in July to federal child-pornography charges and was sentenced earlier this month to 60 years in prison. He also pleaded guilty to first-degree state sexual-abuse charges.

In a statement Wednesday, USA Gymnastics said the settlement’s confidentiality was requested by Maroney’s lawyer. “In 2016, McKayla’s attorney at the time, Gloria Allred, approached USA Gymnastics, requesting that the organization participate in a confidential mediation process,” a spokeswoman wrote. “USA Gymnastics cannot speak to the mediation process, which is confidential and privileged under California law.”

The organization said the settlement followed California law. “Although USA Gymnastics is disappointed by today’s filing, we applaud McKayla and others who speak up against abusive behavior—including the despicable acts of Larry Nassar.” Neither Allred nor Maroney’s lawyer John Manly immediately responded to a request for comment on the statement.

Maroney’s lawsuit alleges that the U.S. Olympic Committee knew in the summer of 2015 that USA Gymnastics was forcing Nassar out because of allegations of sexual molestation, but concealed that knowledge, including in testimony before the U.S. Senate.

On Wednesday, Mark Jones, a spokesman for the U.S. Olympic Committee confirmed the organization first learned of the allegations against “a USA Gymnastics physician” in summer 2015, after receiving word from USA Gymnastics. “At that time USA Gymnastics indicated that they were in the process of contacting the appropriate law enforcement agencies,” said Jones.

Added Jones: “We are heartbroken that this abuse occurred, proud of the brave victims that have come forward and grateful that our criminal justice system has ensured that Nasser will never be able to harm another young woman.”

The Journal asked the U.S. Olympic Committee in May if it was aware of settlements between USA Gymnastics and at least one gymnast. They said they were not, and haven’t been able to confirm the settlement since, Jones said.

A spokesman for Michigan State declined to comment.

Maroney, now 22 years old and retired from the sport, went public with allegations against Nassar in a Twitter post in October. She said Nassar began abusing her when she was 13 years old, when she joined the national team, and continued until she stopped competing in 2013, including the night before she competed at the 2012 London Olympics.

Through her lawyer, Maroney declined to comment.

The settlement agreement was signed by Maroney, her lawyer, Allred, former president of USA Gymnastics Steve Penny and a lawyer for the governing body. Allred is not named in the lawsuit—Manly, a California plaintiff’s lawyer who has led much of the litigation related to Nassar, filed the lawsuit on Maroney’s behalf.

Allred declined to comment. A lawyer for Penny declined to comment.

Penny left the organization earlier this year amid criticism of the organization’s handling of the Nassar matter and other sexual-abuse allegations. He received a payout of around $1 million at the time of his departure, the Journal has previously reported.

When he stepped down, Penny said in a statement: “My decision to step aside as CEO is solely to support the best interests of USA Gymnastics at this time. It has been heartbreaking to learn of instances of abuse and it sickens me that young athletes would be exploited in such a manner.”

According to the agreement and a person familiar with the matter, Allred described Maroney’s claims in a demand letter to USA Gymnastics in late May 2016. At that time, there were no public allegations against Nassar, although he had been quietly forced out of USA Gymnastics the previous fall after several national team gymnasts voiced concerns about his treatment.

Both parties agreed to wait until after the 2016 Olympic Games in Rio de Janeiro to begin negotiations on the claims, the person said.

By the time Maroney signed the agreement —on Dec. 30, 2016, according to the settlement—Nassar was in federal custody and USA Gymnastics was under fire for its handling of sexual-abuse allegations, as dozens of women came forward with allegations against Nassar and coaches at gyms across the U.S.

The lawsuit alleges that Maroney was “forced to enter” into a confidential agreement with USA Gymnastics, “after suffering for years from psychological trauma of her sexual abuse at the hands of Nassar, and in need of funds to pay for psychological treatment for her worsening psychological condition.”

The settlement included non-disclosure and non-disparagement provisions, with a fine of more than $100,000 for violating either.

The lawsuit seeks to invalidate those provisions under California law, which prohibits confidential settlements in a civil matter that could be prosecuted as a felony sex offense.

The lawsuit describes Nassar’s alleged abuse in graphic detail. Alone with Maroney in treatment rooms or living quarters at camps and competitions, he would place his fingers in her anus and vagina, she alleged, and at least once “mounted” her while he had an erection.

Maroney’s lawsuit comes at a pivotal time for USA Gymnastics, as it seeks to redeem its reputation and defend itself against multiple lawsuits related to Nassar. In light of Maroney’s settlement payment, scores of young women could have claims for relief.

As national team physician over a 25-year-period, including four Olympic Games, Nassar treated hundreds of elite gymnasts, at national and international competitions and during training camps at the Karolyi Ranch in Texas.

In California, USA Gymnastics is asking a judge to throw out state lawsuits filed against the organization by former national team members. Earlier this month, USA Gymnastics filed a motion in Michigan federal court to dismiss claims filed there against the organization, saying the statute of limitations had lapsed for most of the alleged victims and that the organization wasn’t liable for Nassar’s conduct.

Some of USA Gymnastics’ biggest sponsors have dropped the organization. Hershey’s said last week it will allow its contract to lapse, while Procter & Gamble said the company would evaluate its contract next spring, in light of the sexual abuse allegations. Under Armour is ending its outfitting deal with the governing body two years early, according to a person familiar with the matter.

It isn’t known if any members of USA Gymnastics’ board knew about Maroney’s settlement agreement. Some board members have said that they weren’t aware of settlements made to any athletes in 2016.

USA Gymnastics executives have said they first learned of athlete concerns about Nassar in June 2015, after a coach reported overhearing national team gymnasts at the Karolyi Ranch discussing Nassar’s treatment. The organization conducted a five-week internal investigation into the allegations before reporting the matter to the Federal Bureau of Investigation in late July 2015, the Journal has reported.

—Louise Radnofsky and Sara Germano contributed to this article.