A second top Pentagon official resigned this week after being passed over for a departmental promotion.

Kathryn Wheelbarger served in one of the Pentagon’s top policy jobs before being nominated in February as deputy under secretary of defense for intelligence and security. However, the Senate never took up her nomination, and last week the White House instead submitted for the role Bradley Hansell, a former special assistant to the president and associate director at the Boston Consulting Group.

A former senior administration official told ABC News on Thursday that Wheelbarger likely was passed over for the promotion because she was seen as a holdover from the team who worked for retired Marine Corps Gen. James Matts, President Donald Trump’s former defense secretary who resigned over policy differences with the president in late 2018. The official called Wheelbarger an independent thinker who wasn’t deemed loyal enough to Trump.

In her resignation letter, she wrote that she trusted her colleagues would “continue to be guided by the U.S. Constitution and the principles of our founding, which ensures both our security and our freedom,” according to Reuters, which viewed a copy of the letter and first reported her resignation.

As the acting assistant secretary of defense for international security affairs, Wheelbarger worked extensively with U.S. allies and partners overseas and was respected by lawmakers on both sides of the aisle. Before coming to the Pentagon, she handled the Senate Armed Services Committee’s intelligence portfolio for the then-chairman, John McCain, R-Ariz. She also served as counsel to Vice President Dick Cheney during the Bush administration.

In a statement on Thursday, Defense Secretary Mark Esper said Wheelbarger “brought a wealth of experience and the utmost professionalism to the department throughout her service.”

“Her leadership in support of the National Defense Strategy is evident in the proud accomplishments of her team,” Esper said. “She is someone I got to know well over the last three years, and with sincere appreciation for her many contributions and years of service, I wish Katie the very best in what I’m sure will be a very bright future.”

ABC News analyst Mick Mulroy, former deputy assistant secretary of defense for the Middle East, called Wheelbarger “one of the hardest-working, smartest and most talented people I have worked with in government.”

“She should have been confirmed for the job she so ably did for over a year and half,” Mulroy said. “She is a consummate professional who undoubtedly will be missed by the whole Pentagon policy team.

Wheelbarger is the second senior Pentagon official to resign this week after the department confirmed Elaine McCusker was leaving as deputy under secretary of defense (comptroller) on Tuesday.

McCusker had served as the acting comptroller for more than 18 months and had been nominated by the White House to assume the post, but in March her nomination was withdrawn. At the time, critics alleged that it was done in retaliation for the role she played in the president’s impeachment trial.

Emails from the summer of 2019 showed McCusker had advocated internally for the release of $250 million in aid to Ukraine that had been delayed by the Trump administration and later formed the crux of the Trump impeachment trial. After a long exchange with another official over the implications of withholding the aid, McCusker wrote in an email, “You can’t be serious. I am speechless.”

The resignations also follow questions about the administration’s nomination of retired Brig. Gen. Anthony Tata to a top Pentagon policy job — a nomination swiftly met with opposition on Capitol Hill.

Tata, who has publicly praised the president on Fox News, has received backlash for Islamophobic comments, including portraying former President Barack Obama as a Muslim and “terrorist leader” working to benefit Iran, according to now-deleted Twitter posts viewed by Reuters.

The Council on American-Islamic Relations issued a statement opposing his anticipated nomination back in April, saying that in a book Tata also falsely claimed young Muslim men in Great Britain engage in the “gang-raping [of] British women as part of their transition to manhood.”

Tata, according to the White House, is currently a senior adviser to Esper.

ABC News’ Lucien Bruggeman contributed to this report.