Rear Adm. Kevin Sweeney was chief of staff for Mattis, and insiders worry that there will now be a lack of institutional knowledge inside the Pentagon.
Another high-ranking Pentagon officer has stepped down from his post weeks after the resignation of U.S. defence secretary General James Mattis.
In a brief statement posted on Saturday evening, Sweeney said: "I've decided the time is right to return to the private sector".
During Sweeney's time in the private sector, he was Vice President of Track Patch 1 Corporation and served on various boards.
In last night's statement, Sweeney made no mention of the President but a source told CNN the White House actually forced the retired Navy Admiral out of the door.
"Because you have the right to have a secretary of defence whose views are better aligned with yours on these and other subjects, I believe it is right for me to step down from my position", he wrote.
Trump said he moved Mattis' departure date up to January 1, two months earlier than originally planned.
General Mattis's departure coincided with the resignation of Chief Pentagon Spokeswoman Dana W White on Monday.
Mattis stepped down last month after Trump chose to withdraw troops from Syria, writing in a searing resignation letter that Trump should find a replacement whose "views are better aligned with yours" on issues like respecting allies and recognising enemies.