In a statement, the FTSE 100-listed firm said the SFO has charged it with two offences of conspiring with "certain former senior officers and employees of Barclays to commit fraud by false representations".
Mr Varley, former senior investment banker Roger Jenkins, Thomas Kalaris, a former chief executive of Barclays' wealth division, and Richard Boath, the ex-European head of financial institutions, have all been charged with conspiracy to commit fraud in the June 2008 capital raising.
The Serious Fraud Office charges come at the end of a five-year investigation and relate to the bank's fundraising at the height of 2008's financial crisis.
Barclays, Varley and Jenkins were charged with another count in regard to a second capital raising in October 2008. A London court hearing is scheduled for July 3.
"The SFO has informed Barclays that it has not made a decision as to whether it will also bring charges against Barclays Bank Plc in respect of the loan".
Barclays said it is "considering its position in relation to these developments".More news: Cristiano Ronaldo haircut was to fulfil Champions League promise
In one of the many ironies of the crisis, none of the executives at RBS and Lloyds at the time has faced criminal charges - a matter of much resentment among taxpayers who picked up the 53 billion pound check for the bailouts.
The charges come almost five years after the SFO opened its case.
It added that the City watchdog, the Financial Conduct Authority (FCA), had reopened its investigation while U.S. authorities were continuing their own inquiries.
Mr Varley, 61, was appointed Barclays's CEO in 2004 after starting his career at the bank in the 1980s.
The U.S Department of Justice and the Securities and Exchange Commission are also investigating the payments made to Middle Eastern officials.
A spokesman for the Qatar Investment Authority declined to comment.