Four former bosses at Barclays are the first executives to face charges over the way they handled the financial crisis for the company nearly 10 years ago.
It marks the first criminal charges to be brought in the United Kingdom against a bank and its former executives for activities during the financial crisis.
Rio said in a statement on Wednesday that Mr Varley had resigned with immediate effect, but did not mention the charges.
Varley and another senior executive Roger Jenkins were charged with conspiracy to commit fraud by false representation in relation to a first round of investment in June 2008.
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The charges relate to a five-year investigation dating back to the Global Financial Crisis when Mr Varley was the chief executive of the investment big bank, Barclays.
Mr Varley was the chief executive officer at Barclays when the bank - along with several other big financiers such as Lloyds and the Royal Bank of Scotland - faced collapse and potential nationalisation.
The defendants and a bank representative will appear at Westminster Magistrates Court on July 3.
According to Jenkins' lawyer, he will be looking to fight the case and "vigorously defend" himself and that he already received inter and external legal advice as of late.
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The suspicion is charges have been framed against Barclays Bank plc, the holding company rather than the business running the bank's day-to-day trading to encourage a guilty plea. "I repeatedly raised concerns about the decisions taken by the bank with both senior management and senior lawyers and was reassured that those decisions were lawful".
Rio Tinto director John Varley has stepped down from the mining giant's board after being charged in a high-profile United Kingdom corruption investigation.
It added that the City watchdog, the Financial Conduct Authority, had reopened its investigation while U.S. authorities were continuing their own inquiries.
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