The bank provided no reason for Hopkinson's departure.
Cristina Alba Ochoa will act as interim chief financial officer from Jan. 15 and the bank has started looking for a permanent successor, it said in a filing.
Metro Bank launched in 2010 aiming to challenge the dominance of Britain's big banks but the lender has suffered a string of setbacks, such as accounting errors, leadership departures and delayed regulatory approval for key capital relief trades.
In October, it announced a 325 million pound ($415 million) capital raising and 600 million pound in debt refinancing, after urgent negotiations to bolster its balance sheet.
In November, the bank announced cost-cutting plans.
($1 = 0.7836 pounds)
(Reporting by Eva Mathews in Bengaluru; editing by Rashmi Aich and Jason Neely)