The 68-year-old was charged alongside another man and a woman, both 52, at Hammersmith Police Station yesterday, Scotland Yard said.
All three are accused of sex offences, said to have happened in the 1990s, against the same alleged victim, then aged between 12 and 15. They will appear at Westminster Magistrates’ Court next week.
Shah told the Swindon Advertiser that he was “really stunned” after being informed by his legal team that he was to be charged.
He said: “I am innocent and I am going to fight this all the way and clear my name.
“I am at a loss to understand why this is happening. It is going to be very hard on me and my family but they are supporting me and I will fight on.”
Shah, whose real name is Selim Shah, founded the now-defunct Today newspaper in 1986.
A local publisher before that, he confronted the trade unions at his Warrington print works and Manchester news offices and became the first person to invoke Margaret Thatcher’s Anti-Union Laws to force unions to the bargaining table.
According to his website, he has moved into the property and leisure building business with wife Jennifer, and runs the Wiltshire Golf Country Club and Hotel in Wootton Bassett, Wilts.
The 200-acre hotel, leisure centre and golf club is for sale for £3.5 million, the Swindon Advertiser reported.
Shah was arrested in September last year with four other people in relation to allegations of sex with an underage girl.
Yesterday Shah, from Chippenham, Wiltshire, was charged with seven counts of rape of a female under the age of 16, and two counts of gross indecency with a girl under 14, Scotland Yard said.
The charges - faced jointly with the woman - are alleged to have happened between 1993 and 1995.
Scotland Yard said Anthony Pallant, of West Malling, Kent, was charged with two counts of rape of a female under the age of 16, and one count of indecent assault on a girl under 14.
He also faces four counts of gross indecency with a girl under 16, jointly charged with the woman. The alleged offences are said to have happened on various dates between 1991 and 1994.
The accused woman, from Kent, who police did not name, was charged with one count of indecent assault on a girl under 14 and was also charged jointly with Pallant of four counts of gross indecency with a girl under 16.
She also faces two counts of gross indecency with a girl under 16 - charged jointly with Shah - and seven counts of aiding and abetting the rape of a female under the age of 16 by Shah. The charges are alleged to have occurred on various dates between 1991 and 1995, Scotland Yard said.
All three were bailed to appear at Westminster Magistrates’ Court on June 7 at 9.30am.