Trump said in a post on Truth Social that he would nominate former Lieutenant General Dan "Razin" Caine to succeed Brown, breaking with tradition by pulling someone out of retirement for the first time to become the top military officer.
Trump will also replace the head of the US Navy, a position held by Admiral Lisa Franchetti, as well as the Air Force vice chief of staff and judge advocates general for the Army, Navy and Air Force, the Pentagon said.
The decision sets off a period of upheaval at the Pentagon, which was already bracing for mass firings of civilian staff, a dramatic overhaul of its budget and a shift in military deployments under Trump's new America First foreign policy.
While the Pentagon's civilian leadership changes from one administration to the next, the uniformed members of the US armed forces are apolitical, serving the policies of Democratic and Republican administrations.
Brown became the highest-ranking military officer in October 2023 and was serving a four-year term due to end in September 2027.
A US official said Brown was relieved with immediate effect before the Senate confirmed his successor.
Democratic lawmakers condemned Republican Trump's decision.
"Firing uniformed leaders as a type of political loyalty test, or for reasons relating to diversity and gender that have nothing to do with performance, erodes the trust and professionalism that our service members require to achieve their missions," the Senate Armed Services Committee's top Democrat Jack Reed said.
Representative Seth Moulton, a Massachusetts Democrat, said the firings were "un-American, unpatriotic, and dangerous for our troops and our national security".
"This is the definition of politicising our military," he said.
Trump did not explain his decision to replace Brown.
"I want to thank General Charles 'CQ' Brown for his over 40 years of service to our country, including as our current Chairman of the Joint Chiefs of Staff," Trump wrote.
"He is a fine gentleman and an outstanding leader, and I wish a great future for him and his family."
Defence Secretary Pete Hegseth, a former Fox News personality and military veteran, had been sceptical of Brown before taking the helm of defence with a broad agenda that includes eliminating diversity, equity and inclusion initiatives in the military.
In his 2024 book The War on Warriors: Behind the Betrayal of the Men Who Keep Us Free, Hegseth asked whether Brown would have gotten the job if he were not Black.
"Was it because of his skin colour? Or his skill? We'll never know, but always doubt - which on its face seems unfair to CQ. But since he has made the race card one of his biggest calling cards, it doesn't really much matter," he wrote.
A former fighter pilot and only the second Black officer to become chairman of the Joint Chiefs of Staff, Brown recounted his experiences in an emotional video posted online after the 2020 killing of George Floyd.
Hours before Trump's post, Brown's official X account had posted images of him meeting troops on the US border with Mexico.
"Border Security has always been critical to the defence of our homeland. As we navigate unprecedented security challenges ... we will ensure our troops at the border have everything they need," he said in a post on X.
A spokesperson for Brown did not immediately respond to a request for comment.Â
