The exit of Craig Donaldson comes amid a difficult time for the lender, which revealed a £900m accounting error in January this year.
The CEO of Metro Bank is standing down amid a difficult period for the lender.
He will remain an adviser to the board until the end of next year.
The announcement of Donaldson's departure comes just weeks after the exit of Metro Bank founder and Chairman Vernon Hill, who resigned with immediate effect.
The lender is now on the hunt for a replacement, saying it will consider internal and external candidates.
In the interim, Dan Frumkin, who joined Metro Bank in September this year, has been appointed interim CEO from January 1 next year.
The exit of Donaldson comes amid a troubling period for the lender, whose shares have crashed since it revealed a £900m accounting blunder in January this year.