The bank itself faces the same charge while Barclays, Varley and Jenkins also face a charge relating to fundraising in October 2008 and are accused too of providing unlawful financial assistance.
The trial of four former Barclays executives charged with fraud in relation to emergency fundraisings in 2008 has been scheduled for January next year.
They are the first senior bankers to face criminal charges in relation to events dating back to the banking crisis nearly a decade ago, when Barclays raised £11.8bn in emergency funds from a number of big investors, including Qatar.
One was used by the then-Qatari prime minister, Sheikh Hamad bin Jassim bin Jaber al-Thani, and a $3bn (£2.3bn) loan advanced to Qatar in November 2008. Boath and Kalaris each face one fraud count between May and August over the June capital raising.
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The former executives and Barclays have been charged with conspiracy to commit fraud by false representation related to the June 2008 fundraising.
The charge alleges they conspired together with Barclays Plc "to commit fraud by making a false representation, namely within documents relating to Barclays" capital raising of October 2008, intending to make a gain, namely or cause loss to another, or exposing another to a risk of loss'.
Judge Mr Justice Edis set a date for the trial, which is expected to last up to four months, of January 9 2019.
Varley, who appeared in court wearing a grey suit and green tie, was chief executive between 2004 and 2011. Jenkins is a former head of Middle East and north African investment banking and Boath is a former head of the bank's European financial institutions group.