The Canadian-born musician, who became an American citizen earlier this year, responded to a second clip showing "Like a Hurricane" playing, writing, "I stand in solidarity with the Lakota Sioux & this is NOT ok with me."
Mount Rushmore is located in South Dakota's Black Hills, which is a sacred area to the Lakota Sioux. Native Americans protesters attempted to block the president's path to the event.
This isn't the first time Trump has been called out for using music against artist's wishes. In June, Tom Petty's family spoke out against the use of the late rocker's classic song "I Won't Back Down" during the president's rally campaign rally in Tulsa, Oklahoma.
Numerous other artists have also asked the president to cease-and-desist from using their music at his events, including R.E.M., Rihanna, Pharrell, Guns N' Roses and Steven Tyler.
Young has been battling with Trump over the use of "Rockin' in the Free World" for the past five years. Trump, whose campaign purchased a license for the song, first played "Rockin' in the Free World" after announcing his plans to run for president in 2015.