The musician also said he “stands in solidarity” with Lakota Sioux, who have long claimed the land as their own.
Mount Rushmore sits on territory that was unceded in treaties in the Black Hills from 1851 and 1868.
Despite protests breaking out ahead of the president’s arrival, he proceeded with the Independence Day event and used Young’s songs “Rockin’ in the Free World” and ”Like a Hurricane”.
“This is NOT ok with me…” a tweet posted from Neil Young Archives wrote alongside footage from the event.
He added in a follow-up post: “I stand in solidarity with the Lakota Sioux & this is NOT ok with me.”
Trump also played “Cowgirl in the Sand”, but Young is yet to comment on its usage.
The music of Young, who called Trump a “disgrace to my country” in a searing open letter written in February, has previously been used without his permission.
In 2015, he played “Rockin’ in the Free World” while announcing his presidential bid without seeking musician’s permission.
“Donald Trump was not authorised to use ‘Rockin’ In The Free World’ in his presidential candidacy announcement,” an official statement from Young’s camp said to The Hollywood Reporter.
The tribe said the lack of government-to-government consultation on the event was a primary motivator for the vote.