Cox was attacked with a knife and a firearm outside her constituency surgery in the village of Birstall, northern England, today.
Her murder has sent shockwaves through British politics and drawn messages of condolence from around the world, with US President Barack Obama condemning the "heinous" attack.
Campaigning ahead of Thursday's closely-contested referendum on Britain's membership of the European Union remains suspended Saturday as a mark of respect.
Mair, 52, who is from Birstall, a quiet village in the Yorkshire hills, was arrested Thursday close to the scene of the attack.
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Mair is due to appear in a central London court later Saturday.
"We have now charged a man with murder, grievous bodily harm, possession of a firearm with intent to commit an indictable offence and possession of an offensive weapon," he said.
"Thomas Mair, 52, of Birstall, will appear at Westminster Magistrates Court today."
Prime Minister David Cameron and opposition Labour leader Jeremy Corbyn laid bouquets at a massive floral tribute to Cox in Birstall on Friday.
"Today our nation is rightly shocked," he said.
The White House said Obama offered condolences to Cox's widower and praised her "selfless service".
Obama called Brendan Cox while travelling on the Air Force One presidential plane.
"President Obama offered his sincere condolences on behalf of the American people to Mr Cox and his two young children, as well as to her friends, colleagues and constituents," the White House statement said.
Cox, a former aid worker who was campaigning for Britain to stay in the EU and also spoke out for Syrian refugees, was killed just a few miles (kilometres) from where she was born.