"It's my honor to do it. It's about time," Trump said during the ceremony in the Oval Office.
“He was treated very rough, very tough,” Trump said of Johnson on Thursday as he signed the pardon.
In 1913, Johnson, a noted boxing legend, was convicted by an all-white jury with violating the Mann Act after transporting a white woman he was dating across state lines for “immoral purposes.”
He served one year in prison.
Under the Obama administration, the Department of Justice opted not to recommend a posthumous pardon for Johnson.
On Thursday, McCain applauded the pardon.
"President Trump's action today finally closes a shameful chapter in our nation’s history and marks a milestone that the American people can and should be proud of,” McCain said in a statement.
Last month, Trump tweeted that "Sylvester Stallone called me with the story of heavyweight boxing champion Jack Johnson," the president tweeted Saturday. "His trials and tribulations were great, his life complex and controversial. Others have looked at this over the years, most thought it would be done, but yes, I am considering a Full Pardon!"
ABC News' Meridith McGraw and Halimah Abdullah contributed to this story.