Associate Attorney General Rachel Brand would have inherited oversight of a probe into possible Trump campaign links to Russian interference in the 2016 election if the president forced out the Justice Department's number two, Deputy Attorney General Rod Rosenstein.
Trump and Republican legislators have stepped up attacks on the agency over Special Counsel Robert Mueller's probe.
"I am proud of what we have been able to accomplish over my time here."
Brand, 44, was named to the Justice Department by then president George W Bush in 2003, and left four years later to work in the private sector.
In 2012, president Barack Obama -- a Democrat -- appointed her to the Privacy and Civil Liberties Oversight Board, which reviewed the legality of the National Security Agency's surveillance programs, especially its data collection on US citizens, which Brand defended.
She rejoined the Justice Department in May, appointed by Trump and working directly below Rosenstein and Attorney General Jeff Sessions, who recused himself from involvement with the Mueller probe due to his own work for the Trump campaign.
Sessions praised Brand in a statement, saying she had "shown real leadership over many important divisions at the department."
Trump, frustrated by the Russian investigation, has reportedly considered firing Rosenstein, the only person empowered to dismiss Mueller.
A recent memo from congressional Republicans took aim at Rosenstein for his role in obtaining wiretap warrants on a member of the Trump campaign who had numerous Russian contacts, which the memo described as an abuse of power.
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