Bree Newsome climbed the 30ft steel pole just after dawn despite police telling her to come down, Associated Press reported.
The woman was arrested afterwards along with a man who had entered the fenced area surrounding the base of the flagpole.
There have been calls for the Confederate flag to be removed since nine people were killed in a racist attack in Charleston.
Shooting suspect Dylann Roof had been pictured with the Civil War era saltire – seen by some as a symbol of slavery and racism – on a number of occasions.
Since the pictures emerged there has been pressure to remove the Confederate flag from the memorial in front of the South Carolina State House.
It was first flown in 1962 in protest at the growing civil rights movement and has been a source of rancor and controversy in the state ever since.
The hashtag #TakeItDown has been trending on Twitter in the US.
White House spokesman Eric Schultz has said President Obama believes the Confederate flag “belongs in a museum”.
Bree Newsome describes herself on Twitter as a filmmaker, singer, songwriter and freedom fighter.
A rally by Confederate flag supporters was also scheduled on June 27.
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