Wray raised concerns about an impending inspector general report about the actions of FBI officials when the bureau was investigating both Democrat Hillary Clinton and Republican Donald Trump during the 2016 presidential election, the report said. "Any specifics, I can tell you, none of this decision was made by that of the White House".
Trump has also said McCabe is "racing the clock to retire with full benefits".
Press Secretary Sarah Huckabee Sanders said: "The President wasn't part of this decision-making process".
Various sources described McCabe's departure as a mutual decision, while others said it was the result of pressure to step down.
Another source familiar with the matter said it was a "mutual" decision.
Last week, The Washington Post reported that after James Comey was sacked in May 2017 and McCabe assumed the director's job on an acting basis, the president asked him in a private discussion whom he had voted for in the presidential election. McCabe had repeatedly come under fire from Republicans in Congress and from President Trump. "90 days to go?!" Reports say that McCabe is leaving his position ahead of a previously planned retirement this spring.
McCabe oversaw the investigation into former Secretary of State Hillary Clinton's use of a private email server.
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His issue with McCabe stems from his wife's failed run for the Virginia state Senate in 2015.
Republicans charge that an anti-Trump bias exists in the bureau's ranks, citing the campaign donations to McCabe's wife and, more recently, the release of hundreds of text messages between FBI counterintelligence agent Peter Strzok and FBI lawyer Lisa Page.
The story, which came out during the 2016 campaign, colored Trump's view of McCabe and led him, according to The Washington Post, to ask McCabe who he voted for in the 2016 election.
"I don't think so. No".
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. McCabe's exit follows WaPo's report by one week.
Axios reported last week that Wray threatened to resign if President Trump ordered him to fire McCabe. Baker was reassigned late past year.
The president had thrown jabs at McCabe in a manner unusual for a president and a top Federal Bureau of Investigation official.