D.C. Council member Harry Thomas Jr. agreed Friday to repay the District $300,000 to settle a city lawsuit that alleged he diverted public funds from youth programs and used some of the money to pay for luxury cars and expensive trips.

In a settlement that will avert a civil trial but does not shield the Ward 5 Democrat from possible criminal prosecution, he also agreed not to head up any charitable organizations for at least five years.

Although Thomas did not admit wrongdoing, the settlement underscores the growing legal and political pressures facing several high-profile District leaders accused of ethical misconduct. The case also stands as a significant early accomplishment for the city’s new attorney general, Irvin B. Nathan, who has stressed that he will aggressively pursue allegations of mismanagement or corruption at city hall.

“Our unrelenting persistence in bringing and prosecuting this action demonstrates our commitment to pursue anyone, no matter his or her station or influence, who would deprive the city of its precious resources,” said Nathan, who was the House of Representatives’ chief counsel on Capitol Hill before becoming the city’s top lawyer in January.

Thomas did not return calls seeking comment Friday, but he issued a statement saying that he settled the lawsuit “in the best interest of the city.”

“I have used my role as a council member to tend to the needs and interests of those who I have the privilege to serve,” he said. “These actions are being taken to ensure that the trust the public has placed in me is maintained and honored.”

But the settlement will likely renew calls for the two-term council member to resign from a body hobbled by several recent ethical controversies.

In June, following an investigation initiated by former attorney general Peter Nickles, Nathan filed a civil suit against Thomas in D.C. Superior Court, alleging that about $392,000 in city funds for “youth baseball programs” was given to an organization that had close ties to Thomas. That group then diverted about three-quarters of the money, totaling just over $300,000, to a nonprofit entity, Team Thomas, which Thomas controlled.

According to the lawsuit, Team Thomas used some of the money to purchase a $59,000 Audi sport-utility vehicle for Thomas and pay for vacations to Las Vegas and Pebble Beach, Calif.

Friday was the deadline for Thomas to formally respond to the suit, which sought $1 million for repayment of the grant money in addition to damages, attorneys’ fees and other costs.

After several weeks of on-again off-again settlement talks, Nathan said his office and Thomas’s attorneys struck a deal late Thursday to settle the case.

Thomas neither admits nor denies guilt under the terms of the settlement. But Thomas, son of the late three-term Ward 5 council member Harry Thomas Sr., delivered a $50,000 cashier’s check to the D.C. treasurer’s office Friday afternoon as part of the deal. Thomas, who makes $125,583 annually as a council member, will also have to make five additional $50,000 payments to the city by Dec. 31, 2013, according to documents filed with the D.C. Superior Court. Thomas also has five days to donate sports equipment, valued at $50,000 and in the possession of Team Thomas, to a city-sanctioned youth sports program.

“It’s a complete recovery of all that was diverted, and we did it in six weeks without having to spend a lot of time in court,” said Nathan, who added that the city is prepared to file a lien on Thomas’s assets if the payments are not made.

Nickles, however, said in an interview that the terms of the settlement “seem light” because Thomas did not have to admit wrongdoing or pay damages.

“He will continue to say he is innocent, as he has for months, which is clearly not true,” Nickles said.

Thomas’s chief attorney, Frederick D. Cooke, did not return calls seeking comment Friday. Thomas also appears to have retained high-profile lawyer Abbe David Lowell, who specializes in white-collar criminal investigations, according to court documents. Lowell was not available to comment.

Last month, Nathan recommended that U.S. Attorney Ronald C. Machen consider filing criminal charges against Thomas. Federal prosecutors have confirmed that they are investigating Thomas, and Nathan said the settlement of the civil suit will not give the council member immunity from possible prosecution.

“The attorney general only wanted money back that was stolen from the city,” said Paul Craney, executive director of the D.C. Republican Committee, which initially raised questions about Thomas’s nonprofit during his 2010 reelection campaign. “This should only reinforce the U.S. attorneys and FBI to act sooner rather than later.”

In addition to Thomas, the U.S. attorney’s office is also believed to be looking into allegations of misconduct involving political campaigns overseen by Mayor Vincent C. Gray (D) and D.C. Council Chairman Kwame R. Brown (D).

But city officials and legal experts believe that Thomas could be at most risk for criminal prosecution.

The allegations concern two groups controlled by Thomas, a for-profit business created in 2004 and a now-defunct nonprofit created shortly after Thomas joined the council in 2007.

The nonprofit never obtained federal tax-exempt status, according to the lawsuit, and was not licensed to accept charitable contributions. In 2007, the council voted to budget $400,000 for “youth baseball programs” via the Children and Youth Investment Trust Corp.

Thomas then directed the trust to give it to a foundation run by Langston Golf Course, which the suit alleges had ties to Thomas. The Langston 21st Century Foundation then transferred about $300,000 to Team Thomas. Some of that was used to pay for Thomas’s car and trips. The Langston foundation has agreed to repay the city $86,000.

Last month, following Nathan’s suit, Thomas was forced to step down as chairman of the council’s Economic Development Committee. But Thomas has so far resisted calls from some civic activists that he resign, and only one council colleague — David A. Catania (I-At Large) — has sought his resignation.

“It’s always difficult for legislators to say a colleague should step aside when they have to work together the next day,” said council member Phil Mendelson (D-At Large).

Although Nathan vowed Friday that the District will recoup its money, it wasn’t clear how Thomas planned to repay the debt.

According to 2011 financial disclosures and honoraria statements, Thomas reports no income beyond his annual council salary.