If confirmed by the Senate, Milley would succeed retiring Marine Gen Joseph Dunford as chairman of the Joint Chiefs of Staff.
Trump had been expected to make the announcement at the Army-Navy game, but made the announcement on Twitter instead.
This latest shake-up follows the announcements of William Barr as Trump's pick for the next AG and Heather Nauert as United Nations ambassador.
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Trump will attend the Army-Navy football game on Saturday afternoon. Typically, the successor to the chairman would not be selected until next year, given that Dunford is due to serve until October 1, 2019.
He hinted then that he would have an announcement related to the Joint Chiefs of Staff, when speaking with reporters. Previous chairmen served two two-year terms if they were re-nominated. Trump re-nominated him in 2017 for a second term.
Milley will be the first Chairman of the Joint Chiefs of Staff to serve a single 4-year term. He has commanded units with the 10th Mountain Division and the 101st Airborne and served multiple combat tours in Iraq and Afghanistan.