The bank said in a statement Tuesday that "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."
Sants started work at the bank 10 months ago, after five years heading Britain's Financial Services authority through the global banking crisis.
His appointment was part of reforms by Barclays' new chief executive, Antony Jenkins.
Last year, Barclays was fined 290 million pounds ($462 million) for manipulating a key interbank lending rate. CEO Bob Diamond stepped down amid the scandal.