"It's my honor to do it. It's about time," Trump said during an Oval Office ceremony, where he was joined by boxer Lennox Lewis and actor Sylvester Stallone, who has drawn awareness to Johnson's cause.
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Trump said Johnson had served 10 months in prison for what many view as a racially-motivated injustice and described his decision as an effort "to correct a wrong in our history."
"He represented something that was both very beautiful and very terrible at the same time," Trump said.
Johnson was convicted in 1913 by an all-white jury for violating the Mann Act, which made it illegal to transport women across state lines for "immoral" purposes, for traveling with his white girlfriend.
Honoring the 1st Black world heavyweight boxing champ in Galveston
Trump had said previously that Stallone had brought Johnson's story to his attention in a phone call.
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"His trials and tribulations were great, his life complex and controversial," Trump tweeted in April. "Others have looked at this over the years, most thought it would be done, but yes, I am considering a Full Pardon!"
Johnson is a legendary figure in boxing and crossed over into popular culture decades ago with biographies, dramas and documentaries following the civil rights era.
He died in 1946. His great-great niece has pressed Trump for a posthumous pardon, and Sen. John McCain, R-Ariz., and former Senate Majority Leader Harry Reid, D-Nev., have been pushing Johnson's case for years.
The son of former slaves, Johnson defeated Tommy Burns for the heavyweight title in 1908 at a time when blacks and whites rarely entered the same ring. He then mowed down a series of "great white hopes," culminating in 1910 with the undefeated former champion, James J. Jeffries.
McCain previously told The Associated Press that Johnson "was a boxing legend and pioneer whose career and reputation were ruined by a racially charged conviction more than a century ago."
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"Johnson's imprisonment forced him into the shadows of bigotry and prejudice, and continues to stand as a stain on our national honor," McCain has said.
Posthumous pardons are rare, but not unprecedented. President Bill Clinton pardoned Henry O. Flipper, the first African-American officer to lead the Buffalo Soldiers of the 10th Cavalry Regiment during the Civil War, and Bush pardoned Charles Winters, an American volunteer in the Arab-Israeli War convicted of violating the U.S. Neutrality Acts in 1949.
Linda E. Haywood, the great-great niece, wanted Barack Obama, the nation's first black president, to pardon Johnson, but Justice Department policy says "processing posthumous pardon petitions is grounded in the belief that the time of the officials involved in the clemency process is better spent on the pardon and commutation requests of living persons."