Trump tweeted that Flood will step down on June 14.
"Emmet Flood, who came to the White House to help me with the Mueller Report, will be leaving service on June 14th," Trump wrote. "He has done an outstanding job – NO COLLUSION - NO OBSTRUCTION! Case Closed! Emmet is my friend, and I thank him for the GREAT JOB he has done."
Flood, a Washington lawyer who represented former President Bill Clinton during his impeachment proceedings against him in the 1990s, joined the White House last year.
He was expected to resign after Mueller concluded his investigation into potential ties between Russia and the Trump campaign. In April, Mueller released his 448-page report on his probe.
Flood criticized Mueller in a five-page letter dated April 19 in which he reacted to his final report for not reaching a final conclusion regarding potential obstruction of justice charges against Trump.
“The Special Counsel and his staff failed in their duty to act as prosecutors and only as prosecutors,” Flood wrote, complaining that the report "suffers from an extraordinary legal defect" by failing to comply with the "requirements of governing law."
The report showed Mueller was unable to prove ties between Russia and the Trump campaign. He declined to make a determination about whether Trump committed obstruction of justice.