The charge relates to IS’s status as a “proscribed terrorist organisation”, meaning supporting it is banned in Britain.
Charged alongside the Muslim campaigner is Mohammed Mizanur Rahman.
A statement from Crown Prosecution Service said the charges relate to the two men’s activities between 29 June 2014 and 6 March this year.
Choudary, 48, of Hampton Road, Ilford in east London, was due to appear at Westminster Magistrates’ Court at 2pm on Wednesday.
Sue Hemming, Head of Special Crime and Counter Terrorism at the CPS, said: “Following an investigation by the Metropolitan Police’s Counter Terrorism Command, we have today authorised charges against Anjem Choudary and Mohammed Mizanur Rahman.
“We have concluded that there is sufficient evidence and it is in the public interest to prosecute Anjem Choudary and Mohammed Rahman for inviting support for ISIL (IS), a proscribed terrorist organisation, between 29 June 2014 and 6 March this year.
“Each man is charged with one offence contrary to section 12 of the Terrorism Act 2000.
“It is alleged that Anjem Choudary and Mohammed Rahman invited support for ISIS (IS) in individual lectures which were subsequently published online.
“The decision to prosecute was taken in accordance with the Code for Crown Prosecutors.
“Anjem Choudary and Mohammed Rahman will appear at Westminster Magistrates’ Court later today, 5 August 2015.
“Criminal proceedings have now commenced and both men have a right to a fair trial.
“It is extremely important that there should be no reporting, commentary or sharing of information online which could in any way prejudice these proceedings.”
Section 12 of the Terrorism Act 2000 says that a person commits an offence if they invite “support for a proscribed organisation, and the support is not, or is not restricted to, the provision of money or other property.”
It says that a person can face up to 10 years in jail if found guilty.
The Home Office moved to ban Islamic State, which it calls Islamic State in Iraq and the Levant (ISIL) in June last year.