Andrew McCabe was forced to step down ahead of his official retirement date in March.
His exit from the top law enforcement agency comes a week after a report that Mr Trump wanted him out.
It was also reported last week that the president had asked Mr McCabe during an Oval Office meeting whom he voted for.
White House press secretary Sarah Huckabee Sanders told Monday's daily press briefing: "This decision was not made by the White House."
"The president wasn't part of this decision making process," she added.