The bank is investigating how two million accounts were opened without customers’ permission.
In September, it said John Stumpf, who was paid $19.3 million in 2015, would not receive a salary during the inquiry.
John Stumpf will be succeeded by the bank’s current president and chief operating officer, Timothy Sloan.
Wells Fargo’s independent chairman, Stephen Sanger, will take over as board chairman.
Last month, the bank was fined $185 million and accused of “widespread illegal practice” by the US Consumer Financial Protection Bureau (CFPB).
The fine imposed on Wells Fargo by the CFPB was the largest to date by the watchdog.
“While I have been deeply committed and focused on managing the company through this period, I have decided it is best for the company that I step aside,” John Stumpf said.
The bank has fired more than 5,000 staff in response to the scandal.
Wells Fargo has said it will be contacting every deposit customer across the country to see if their accounts were properly authorized.
The bank will also contact hundreds of thousands of customers with valid credit cards to see if they want or need those cards.
In the future, confirmation emails will be sent to customers within one hour of the opening of a new deposit account.
Wells Fargo’s former head of retail operations, Carrie Tolstedt, has forfeited $19 million of bonuses and left without a payoff.
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