Choudary, 56, has been charged with membership of a proscribed organization, directing a terrorist organization, and addressing meetings to encourage support for a proscribed organization, police said. He will appear in court in London on Monday.
Once Britain's most high-profile Islamist preacher, Choudary was imprisoned in Britain in 2016 for encouraging support for Islamic State before being released in 2018 after serving half of his five-and-a-half-year sentence.
Choudary, former head of the now-banned organization al-Muhajiroun, drew attention for praising the men responsible for the 9/11 attacks on the United States and saying he wanted to convert Buckingham Palace into a mosque.
His followers have been linked to numerous plots across the world.
A 28-year-old Canadian man, Khaled Hussein, has also been charged with membership in a proscribed organization after being arrested on the same day as Choudary when he arrived on a flight at Heathrow Airport, police said.