"As he steps down to reenter the private sector, we’re going to miss him here in the Pentagon. We know great things are in store for him and his family," Shanahan said.
Defense Secretary Chief of Staff Kevin Sweeney served in this role since January 2017.
"After two years in the Pentagon, I've decided the time is right to return to the private sector. It has been an honor to serve again alongside the men and women of the Department of Defense," Sweeney was quoted in a DoD statement.
CNN earlier reported that Sweeney was forced out by the Trump White House. His resignation follows closely that of US Secretary of Defense James Mattis who stood down earlier this month after acknowledging policy differences with the US president.
