Liam Coleman oversaw a restructuring and recapitalisation plan with U.S. hedge fund creditors last June, after the Co-operative Bank's capital base fell to levels which were unacceptable to regulators.
Coleman will remain with the Co-operative Bank during the search for a successor, it said in a statement on Thursday.
"I feel a great sense of achievement in how much we have collectively delivered both to address the fundamental issues the organisation faced back in 2013 and to reshape the business around our retail customers," Coleman said.
"This is a great bank with a strong customer base and distinct brand and the progress made means there is much to build upon," he added.
Coleman joined the bank in June 2013 as treasurer. Before his appointment as chief executive in January 2017, he was made deputy chief executive in June 2016.
(Reporting by Dasha Afanasieva; Editing by Ben Martin and Alexander Smith)