UK-born Choudary, 48, was charged along with Mohammed Rahman, 32, with inviting support for a proscribed terrorist organisation, namely Islamic State in Iraq and the Levant (ISIL).
"It is alleged that Anjem Choudary and Mohammed Rahman invited support for ISIS (also known as ISIL) in individual lectures which were subsequently published online, said Sue Hemming, of the Crown Prosecution Service (CPS).
"Each man is charged with one offence contrary to section 12 of the Terrorism Act 2000," Hemming said.
Both appeared before Westminster Magistrates' Court today but details of the hearing are yet to be released.
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Choudary, of Ilford in east London, and Rahman, of Whitechapel in east London, were arrested on September 25 last year on suspicion of being members of ISIL.
Proscription means membership of the militant group is a criminal offence, and that the organisation cannot lawfully operate in the UK.
UK media regulator Ofcom also launched an investigation into interviews broadcast on BBC, ITV and Channel 4 with Choudary in the days following the murder of Fusilier Lee Rigby on the streets of London in May 2013.