Like many of her predecessors, the first lady has been known to share her private views about staff with the president but broke with tradition when her office called for him to dismiss Mira Ricardel.
"The president is grateful for Ms. Ricardel's continued service to the American people and her steadfast pursuit of his national security priorities", said White House press secretary Sarah Huckabee Sanders.
Ricardel has also built a reputation in the White House for berating staff, several sources said.
Her behavior surrounding Melania Trump's solo trip to Africa in October also reportedly irked the first lady, which Noah couldn't help but poke fun at during his segment on Wednesday night.
National security adviser John Bolton, who was in Singapore when news of Ricardel's dismissal broke, said when he tapped her to be his deputy in April that she "has a track record of successfully managing teams and diverse organizations, as well as addressing complex issues".
Nick Ayers, a 36-year-old chief of staff to Vice President Mike Pence and renowned political consultant, is reportedly high on the list to replace Mr Kelly. Ricardel blocked some of his picks for Pentagon positions because they included former Obama administration officials who she felt were not strict Republican loyalists, multiple defense officials have told CNN.
He said on Wednesday in an interview with the Daily Caller that he'll soon "be making a decision" on Homeland Security Secretary Kirstjen Nielsen, who has reportedly fallen out of favour with the president over what he's described as an illegal immigration "crisis" at the USA border with Mexico.
"A lot of people want to come in, a lot of politicians who have had very successful careers want to come in", he said. It was not yet clear what her new position would be.
Trump has been in a funk since last week's midterms which saw the Democrats seize control of the House of Representatives, ending the Republicans' dominance of both chambers of Congress. But issuing a statement calling for an administration official to be fired before any such announcement has been made by the White House was an extraordinary move, regardless of personal tensions.
When Mr Trump suddenly replaced his attorney general Jeff Sessions last week with a fierce critic of the Russian Federation investigation, Matthew Whitaker, critics accused him of violating the constitution.