As expected he will take accumulated leave and remain on the payroll until March when he is eligible to retire with full benefits.
One source said Monday's departure was not in the plans as of Friday.
Yet as recently as last month, Trump seized on McCabe's role in the Clinton inquiry and his wife's political bid, noting that Jill McCabe received almost $470,000 from a political action committee associated with Clinton ally and Virginia Gov. Terry McAuliffe.
His departure comes roughly a week after news emerged that Trump asked McCabe who he voted for during an introductory meeting in May - not long after Comey was abruptly fired. Asked about how people should view Trump's frequent Twitter tirades against McCabe, Sanders said the President is simply doing the public a favor.
In recent weeks, McCabe has been questioned by the House Oversight and Government Reform Committee, the House Judiciary Committee and the House Intelligence Committee.
USA official urges Turkey to halt Syria campaign
But Turkey considers the YPG as part of the long Kurdish insurgency for an independent Kurdistan which would include part of Turkey.
The FBI has said McCabe received the necessary ethics approval before his wife received the donations and that at the time of the contributions, he was not in a supervisory role of the FBI's investigation into Hillary Clinton's email use.
Press Secretary Sarah Huckabee Sanders pushed back against suggestions that President Trump had anything to do with McCabe's ouster.
Another source familiar with the matter said it was a "mutual" decision. "90 days to go?!".
In recent months, McCabe has been harshly criticised by congressional Republicans who challenge the FBI's rationale for opening the Russian Federation probe back in July 2016. "I would say a man who is more or less in charge of her, the wife got $500,000 from Terry. I wasn't there. There are widespread reports of his retirement".
Gaetz has scrutinized what he and other Republicans perceive to be a tilt toward Hillary Clinton in the 2016 campaign from the Federal Bureau of Investigation and the Department of Justice, and McCabe stepping down will allow the White House to select someone more attuned with Republican views on these organizations.