"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 posted on social media. He said five other top officers were being replaced.
Gen Brown was the second black officer in US history to hold the post, which advises both the president and the secretary of defence on national security.
Defence Secretary Pete Hegseth had previously said that Gen Brown should be fired because of his "woke" focus on diversity, equity and inclusion programmes in the military.
Later on Friday, Hegseth announced the firings of two additional senior officers: Chief of Naval Operations Adm Lisa Franchetti and Vice Chief of Staff of the Air Force Gen Jim Slife.
Adm Franchetti was the first woman to lead the Navy.
All three top officers removed on Friday were appointed by former President Joe Biden.
Hegseth said in a statement: "Under President Trump, we are putting in place new leadership that will focus our military on its core mission of deterring, fighting and winning wars."
Trump said he would nominate Air Force Lt Gen Dan Caine - a career F-16 pilot who most recently served as CIA associate director for military affairs - as the new chairman of the joint chiefs of staff.
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