Federal district judges in Manhattan on Wednesday appointed James M. McDonald, a former partner at Sullivan & Cromwell who represented President Trump in his appeal of his criminal conviction, to lead the U.S. attorney’s office for the Southern District of New York.

Mr. McDonald, a former federal prosecutor in Manhattan, had already been selected by Mr. Trump to succeed Jay Clayton, the previous U.S. attorney in Manhattan, who on Tuesday was confirmed as the director of national intelligence.

On Wednesday, the district judges in Manhattan ratified the president’s choice, making Mr. McDonald the second judicially appointed U.S. attorney in Manhattan during the president’s second term. (The court installed Mr. Clayton in the post when his interim appointment by Mr. Trump expired last August.)

The court, in a two-paragraph statement, said Mr. McDonald’s appointment became effective with the resignation of Mr. Clayton, who stepped down as U.S. attorney on Wednesday.

In moving quickly to name Mr. McDonald, the court made it clear it did not want the top prosecutor’s post to remain vacant for long, saying in the statement that it was acting “to ensure continuity” in the U.S. attorney’s office. The appointment also comes at a sensitive time for the U.S. attorney’s office, which is handling such high-profile cases as the prosecution of Nicolás Maduro, the former president of Venezuela, who was captured by American military forces in January.

Mr. McDonald’s appointment appears to be moving more smoothly than most court appointments of U.S. attorneys have during the Trump administration. The Justice Department has said it will not tolerate judges’ selecting U.S. attorneys without coordination with the executive branch. Several other U.S. attorneys who have been appointed by judges have been summarily fired by the Trump administration.

Just this month, the administration moved to fire Roger Rogoff, a U.S. attorney who was selected by judges in western Washington to lead the office there. Mr. Rogoff sued the department, arguing that in firing any prosecutor not approved by his administration, Mr. Trump was seeking to circumvent laws that require permanent U.S. attorneys to be confirmed by Congress.

No such conflict is anticipated in the Southern District of New York, where Mr. McDonald is set to take over one of the most high-profile and prestigious posts at the Justice Department. He is a personal friend of Todd Blanche, the acting attorney general, who was also a prosecutor in the Southern District before representing Mr. Trump when the president was facing a series of criminal investigations.

Mr. McDonald, much admired by his fellow office alumni, is often characterized as a likable legal wonk. He clerked for Chief Justice John G. Roberts Jr. and later became a federal prosecutor; he was involved in a number of high-profile cases including the corruption prosecution of Sheldon Silver, the once-powerful Democratic speaker of the New York State Assembly.

Mr. McDonald, during that trial, served as a legal specialist — or, more colloquially, as one of the “law guys” — assisting his team in knotty issues that loom large in corruption cases.

Mr. McDonald went on to lead the enforcement division at the Commodity Futures Trading Commission during the first Trump administration. That experience will most likely be relevant in Mr. McDonald’s new role; a number of insider trading investigations are in progress at the Southern District, thanks in part to the growth of prediction markets, which are regulated by the commission. In 2021, Mr. McDonald went to Sullivan & Cromwell.

At the firm, which last year took over Mr. Trump’s appeal of his 2024 criminal conviction, Mr. McDonald represented Live Nation and Polymarket, both of which received favorable treatment from the Justice Department after having been the subject of federal scrutiny.

This month, Mr. McDonald returned to the U.S. attorney’s office after Mr. Clayton was nominated for his new role. Mr. McDonald was named as the deputy U.S. attorney, the traditional title of the office’s No. 2 position.

While in the office, Mr. McDonald has been involved in a leak investigation centered on New York Times articles related to security vulnerabilities of an Air Force One jet that Qatar had given to Mr. Trump. The investigation resulted in a number of subpoenas being sent to Times reporters, which the Justice Department withdrew after a judge expressed skepticism about whether prosecutors had followed the law.