The Justice Department said on Tuesday it would pay $138.7 million to resolve 139 claims by young women, including many top female gymnasts, of abuse by the former U.S.A. Gymnastics doctor Lawrence G. Nassar.

The far-reaching settlement, which had been expected, stems from the failure of Federal Bureau of Investigation officials to promptly investigate credible claims that Mr. Nassar had sexually assaulted more than 150 women and girls under the guise of examinations and treatment.

It likely marks the end of a yearslong effort by the gymnasts — including the Olympic gold medalists Simone Biles, McKayla Maroney and Aly Raisman — to achieve a measure of justice and public recognition that the institutions entrusted to protect young female athletes failed to protect them.

While lawyers for the young women hailed the settlement, they cast the government’s monetary compensation for its early reluctance to fully investigate Mr. Nassar as a case of too little, too late.

“These women were assaulted because of the F.B.I.’s failure and there is no amount of money that will make them whole again,” said Mick Grewal, a lawyer for 44 of the claimants, including one who died by suicide. “Their goal with all this was to make sure that this never happens again.”

Mr. Grewal said he hoped the deal would “close the book on this and this will help lead them on the path to healing.”

The broad outlines of the agreement were reached late last year. The lawyers have spent months determining the specific payouts, which vary based on the abuse claims but amount to around $1 million per woman or girl, according to two people familiar with the discussions.

Mr. Nassar is serving a 60-year sentence in federal prison in Florida, where he was stabbed multiple times by an inmate in July. He suffered a collapsed lung but survived his injuries.

For victims like Alexis Hazen, who said she was abused by Mr. Nassar from age 12 to 18, a resolution was a long time coming. She reported the abuse in 2016 and she is now 26, married and a mother of three boys.

“I’m relieved but disappointed that no one person is being held accountable for failing to report the abuse and for sweeping it under the rug,” Ms. Hazen said in a telephone interview. “In a way, this helps me be able to move past this, but it’s always in the back of my mind that, wow, if the F.B.I. didn’t protect me, could something like this happen to my children? And that makes me really, really mad.”

“I definitely have no trust in that institution anymore,” she added.

The settlement comes two and a half years after senior F.B.I. officials publicly admitted that agents had failed to take quick action when U.S. national team athletes complained about Mr. Nassar to the bureau’s Indianapolis field office in 2015.

Mr. Nassar, known for working with Olympians and college athletes, has been accused of abusing more than 150 women and girls over the years.

“These allegations should have been taken seriously from the outset. While these settlements won’t undo the harm Nassar inflicted, our hope is that they will help give the victims of his crimes some of the critical support they need to continue healing,” said Benjamin C. Mizer, an acting associate attorney general, who negotiated the settlement.

In 2018, Michigan State University, which employed Mr. Nassar, paid more than $500 million into a victim compensation fund, believed to be the largest settlement by a university in a sexual abuse case. Three years later, U.S.A. Gymnastics and the United States Olympic & Paralympic Committee reached a $380 million settlement.

Many of the girls and women who reported abuse by Mr. Nassar have battled mental health issues, including anxiety, depression and post-traumatic stress disorder, and some have attempted suicide.

A 2021 report by the Justice Department’s inspector general found that senior F.B.I. officials in the Indianapolis field office had failed to respond to the allegations “with the utmost seriousness and urgency that they deserved and required” and that the investigation did not proceed until after the news media detailed Mr. Nassar’s abuse.

F.B.I. officials in the office also “made numerous and fundamental errors when they did respond” to the allegations and failed to notify state or local authorities of the allegations or take other steps to address the threat posed by Mr. Nassar, the inspector general’s report said.

In heart-wrenching testimony two months later, former members of the national gymnastics team described how the F.B.I. had turned a blind eye to Mr. Nassar’s abuse as the investigation stalled and children suffered. Some, including Ms. Raisman, said that agents moved slowly to investigate even after they presented the bureau with graphic evidence of his actions.

The revelations prompted an extraordinary apology from the F.B.I. director, Christopher A. Wray, who did not oversee the bureau when the investigation began. “I am sorry that so many people let you down over and over again, and I am especially sorry that there were people at the F.B.I. who had their own chance to stop this monster back in 2015,” he said.

The settlement is one of several that the Justice Department has reached over the past decade.

The others have involved victims of mass shootings. Families of 26 people killed in a 2017 shooting at a church in Texas received $144.5 million. The mass shooting in 2018 at a high school in Parkland, Fla., resulted in the Justice Department paying families $127.5 million.