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Manning, behind one of the largest classified information leaks in US history, left Fort Leavenworth military prison in Kansas in the morning, Lt. Col. Jennifer Johnson told CNN.
Manning was convicted in 2013 of stealing 750,000 pages of documents and videos pertaining to the wars in Iraq and Afghanistan, as well as sensitive State Department cables before leaking them to WikiLeaks.
In January, former US President Barack Obama commuted Manning's sentence, thereby giving her an early release date.
Amnesty International, which had campaigned for Manning's release, was quick to applaud the decision.
We will continue to call for an independent investigation into the potential human rights violations Manning exposed, and for protections to be put in place to ensure whistleblowers like Chelsea are never again subjected to such appalling treatment," a statement by Amnesty International said.
Last week, Manning tweeted her excitement about her impending release: "Freedom was only a dream, and hard to imagine. Now it's here! You kept me alive <3"
"For the first time, I can see a future for myself as Chelsea. I can imagine surviving and living as the person who I am and can finally be in the outside world," she said in a written statement.
Manning remains on active duty status pending the conclusion of her appeals. As such, she may be entitled to military benefits, including healthcare.