Sir Hector Sants will take a temporary leave of absence after just 10 months in the role as head of compliance at the bank - a post he took on after a gruelling five years at the helm of the Financial Services Authority (FSA) in the run up to and throughout the financial crisis.
A Barclays spokesman said: "Rather than carry on working, and risk more serious consequences to his health, he is following medical advice and will be taking a leave of absence until the end of the year."
He is expected to return to work in the new year and his compliance colleagues will take on his role on an interim basis until then.
Sir Hector is the latest top banking executive forced to take temporary leave after Lloyds Banking Group chief executive Antonio Horta-Osorio took two months off at the end of 2011 due to sleep deprivation and exhaustion.
Sir Hector's role is seen as a crucial part of the overhaul being led by Barclays chief executive Antony Jenkins.
His job involves liaising with regulators and government and to ensure rules are followed at the bank, with responsibility for monitoring questionable trading.
Sir Hector was knighted in the Queen's New Year Honours for services to financial regulation after overseeing sweeping reforms following the nationalisation of Northern Rock and bailout of major banks.
But the knighthood was also seen as a controversial decision, as it was Sir Hector who led the organisation accused by MPs of being "asleep at the wheel" in the run up to the collapse of Northern Rock.
The Oxford graduate , who is married with three children, started his career in 1977 with Phillips & Drew stockbrokers, which was taken over by Swiss banking giant UBS in 1985.
He remained with UBS until 1998 when he joined Donaldson, Lufkin and Jenrette International Securities and then later joined Credit Suisse in 2000.
He became FSA chief executive in 2007.